UD commenter ericB issues a Challenge!!!

I thought I would give a comment by a poster with the handle “ericB” a little more publicity as it was buried deep in an old thread where it was unlikely to be seen by passing “materialists / evolutionists”.

§§§§§§§§§§§§§§§§§§§§

Calling all evolutionists / materialists! Your help is needed! Alan Fox has not been able to answer a particular challenge, but perhaps you know an answer.

The issue is simple and the bar is purposely set low. The question is whether there exists one or more coherent scenarios for the creation of a translation system by unguided chemicals.

The translation system in cells indicates intelligent design. I would submit that, regardless of how many billions of years one waited, it is not reasonable to expect that unguided chemicals would ever construct a system for translating symbolic information into functional proteins based on stored recipes and a coding convention.

[I realize people have thoughts about what happened earlier (e.g. that might not need proteins, for example) and what happened later (e.g. when a functioning cell provides the full benefits of true Darwinian evolution). For the purposes here, attention is focused specifically on the transition from a universe without symbolic translation to construct proteins to the origin of such a system. Whatever happened earlier or later, sooner or later this bridge would have to be crossed on any path proposed to lead to the cells we see now.]

One of the key considerations leading to this conclusion is that a translation system depends upon multiple components, all of which are needed in order to function.

+ Decoding

At the end, one needs the machinery to implement and apply the code to decode encoded symbolic information into its functional form. (In the cell, this is now the ribosome and supporting machinery and processes, but the first instance need not be identical to the current version.) Without this component, there is no expression of the functional form of what the symbolic information represents. The system as a whole would be useless as a translation system without this. Natural selection could not select for the advantages of beneficial expressed proteins, if the system cannot yet produce any. A DVD without any player might make a spiffy shiny disk, but it would be useless as a carrier of information.

+ Translatable Information Bearing Medium

There must be a medium that is both suitable for holding encoded information and that is compatible with the mechanism for decoding. Every decoding device imposes limitations and requirements. It would be useless to a DVD player if your video was on a USB thumb drive the DVD player could not accept instead of a suitable disk. In the cells we see, this is covered by DNA and ultimately mRNA.

+ Meaningful Information Encoded According to the Same Coding Convention

One obviously needs to have encoded information to decode. Without that, a decoding mechanism is useless for its translation system purpose. If you had blank DVDs or DVDs with randomly encoded gibberish or even DVDs with great high definition movies in the wrong format, the DVD player would not be able to produce meaningful results, and so would have no evolutionary benefit tied to its hypothetical but non-functioning translation abilities. In the cell, this information holds the recipes for functional proteins following the same encoding convention implemented by the ribosome and associated machinery.

+ Encoding Mechanisms

This is perhaps the least obvious component, since the cell does not contain any ability to create a new store of encoded protein recipes from scratch. Indeed, this absence is part of the motivating reasons for the central dogma of molecular biology. Nevertheless, even if this capability has disappeared from view, there would have to be an origin and a source for the meaningful information encoded according to the same coding convention as is used by the decoding component.

(For the moment, I will just note in passing that the idea of starting out with random gibberish and running the system until meaningful recipes are stumbled upon by accident is not a viable proposal.)

So there has to be some source capable of encoding, and this source must use the same coding convention as the decoding component. To have a working, beneficial DVD player, there must also be a way to make a usable DVD.

+ Meaningful Functional Source Material to Represent

It would do absolutely no good to have the entire system in place, if there did not also exist in some form or other a beneficial “something” to represent with all this symbolic capability. If you want to see a movie as output, there needs to be a movie that can be encoded as input. If you want functional proteins as output, there needs to be access to information about proper amino acid sequences for functional proteins that can serve as input. Otherwise, GIGO. Garbage In, Garbage Out. If there is no knowledge of what constitutes a sequence for a functional protein, then the result produced at the end of the line would not be a functional protein.

+ Some Other Way To Make What You Want The System To Produce

If we supposed that the first movie to be encoded onto a DVD came from being played on a DVD player, we would clearly be lost in circular thinking, which does not work as an explanation for origins. Likewise, if the only way to produce functional proteins is to get them by translating encoded protein recipes, that reveals an obvious problem for explaining the origin of that encoded information about functional proteins. How can blind Nature make a system for producing proteins, if there has never yet been any functional proteins in the universe? On the other hand, how does blind Nature discover and use functional proteins without having such a system to make them?

The core problem is that no single part of this system is useful as a translation system component if you don’t have the other parts of the system. There is nowhere for a blind process to start by accident that would be selectable toward building a translation system.

The final killer blow is that chemicals don’t care about this “problem” at all. Chemicals can fully fulfill all the laws of chemistry and physics using lifeless arrangements of matter and energy. Chemicals are not dissatisfied and have no unmet goals. A rock is “content” to be a rock. Likewise for lifeless tars.

The biology of cells needs chemistry, encoded information, and translation, but chemicals do not need encoded information or biology. They aren’t trying to become alive and literally could not care less about building an encoded information translation system.

§§§§§§§§§§§§§§§§§§§§§

I’m hoping ericB will find time to respond to any comments his challenge might elicit.

547 thoughts on “UD commenter ericB issues a Challenge!!!

  1. I’m not surprised this “challenge” remained buried in an old thread. It’s so chokker with misconceptions and assumed conclusions as to indicate that the poser hasn’t bothered to learn anything about what non-IDers think about it.
    or what actual working scientists say about it.

  2. FURTHERMORE, I have the deepest objection to the word “symbolic” used in this context – it’s as silly as saying that the substrate for any enzyme reaction is “symbolic” of its product.

  3. I assume you meant poster not poser! I don’t want to give ericB the first impression of being called names. 😯

  4. Alan Fox:
    I assume you meant poster not poser! I don’t want to give ericB the first impressionof being called names.

    No, I meant poser as in “one who poses a challenge”, NOT as in “poseur”.. ericB need not be offended, nor should the sensibilities of the rulers of TSZ be ruffled.

  5. Oops, sorry. “Poser” was a standard insult when I were a lad. “Poseur” on the other hand is something I aspire to on occasion.

  6. Alan Fox:
    Oops, sorry. “Poser” was a standard insult when I were a lad. “Poseur” on the other hand is something I aspire to on occasion.

    I perhaps should have been more careful in my choice of words – you were not wrong to cast a glance at the yellow card, although it would have been an injustice actually to wave it!

  7. + Meaningful Information Encoded

    Ah, Weasel words. Even in the DVD eaxmple there is meaning: wrong format! broken DVD player!

  8. Is it at all strange that an evolved information system would be so different from human-produced information systems? Of course nature could never go about being representational, but what works best tends to survive

    I guess that’s why derivation in life is so evident, and that this derivation is so obviously dependent upon whether or not information transfer processes are vertical-only or are sometimes also horizontal. The fact that nothing knows about all of this information is why vertebrates almost never get to copy good information from other vertebrates which are genetically isolated from them.

    Perhaps he should tell us why life’s “DVD system” can only play one “DVD” and no others for large numbers of organisms. It’s so restrictive, compared with designed information systems.

    Glen Davidson

  9. Is this a reference to attempts to transplant nuclei into the egg cell of another species?

    It does seem odd that the designer had to make the encoding and the player appear as if they had evolved together.

  10. CDK007 made a youtube video years ago that explains how the translation system and the genetic code could have evolved, complete with tRNA, mRNA, ribosomes:

  11. GlenDavidson: It’s so restrictive, compared with designed information systems.

    Indeed. It shows how little the BA’s of this word know about actual programming if they think that “multi-layered codes” with meaning at multiple levels represents something that human designers are striving for.

    And if DNA is a computer program, like those which human programmers create, where are the comments? The self-installing documentation? The tests?

    It seems to me the more I try list similarities, the more differences there are. Which is unexpected if what the IDers claim is true. Where does it leave “the cell is an X and only people make X’s”, the primary claim of ID?

    I went though a phase a few years ago of asking them, when they compared the cell to a computer, to list the equivalents of the ram, cpu etc in a cell. Nobody ever did.

    It’s all about the “information” processing which they can hand off to the likes of KF and Demsbski to produce some “mathy looking math” and job done. ID is proven (there’s math!) and if you don’t accept it it’s because of your ideological blinkers.

    It’d be funny and just a (big) bit sad if they were not strenuously pushing it on children as truth.

  12. I submit that it is perfectly reasonable that evolution could lead to the invention of the DVD player, and that this has in fact happened. I don’t see what DVD players have to do with DNA though.

  13. I’d have to give the briefest of sketches … I’ve spent many moons expounding my views on how protein and the code may have evolved, and I grow weary, grasshopper. I think the fundamental misconception is the belief that the only useful protein is a specified protein, and the only useful specified protein is one with more than a few amino acids in it. This is certainly the case – to some degree – in the case of enzymes, but contrary to popular belief ‘useful protein’ is not synonymous with ‘enzyme’.

    So all one needs at a fundamental level is a non-protein means of catalysing peptide bond synthesis. You don’t need a code to do this; you need a ribozyme. You need another to activate the amino acids, because the reaction will not proceed without energy. This has likely been done all along as it is in modern cells, by aminoacylating nucleic acid bases. Out of this uncoded system will arise a polymer of whatever amino acids went into it. Certain monotonous polymers produce useful structural elements – polyglcyine, for example. Where specificity becomes an issue, one needs a means of ensuring that an amino acid of a particular type (not necessarily a specific acid) occupies a certain position, and to do that biology needs to provide a mechanism to filter a broader set. One way to do this is to use a template, and have the activated amino acids ‘marked’ in some way that binds preferentially with the template. You want to call that symbolic, it’s symbolic. But it isn’t really. Such a basic set can expand – codon groups can subdivide among more acids of similar properties to the ancestral one – until such point that the assignments become embedded in too many critical places to permit further change.

  14. Aside from all the typical ID/creationist misconceptions and misrepresentations in that “challenge” of the way atoms and molecules behave, why should anyone in the science community help ID/creationists with their homework?

    It appears to me to be just another attempt by an ID/creationist to get a free ride without having to think or learn anything. It’s not the fault of the science community that ID/creationists get headaches from brain strain.

  15. I have no answer for ericB. Of course, I am also very ignorant regarding the details scientific findings about most (if not all) aspects of biochemistry, so my lack-of-answer is neither surprising nor should it be taken as an indication of the validity of an entire field of scientific study. But okay, for the purposes of this discussion, let’s say that “evolutionists/materialists” really and truly cannot answer ericB’s question, that there genuinely are no “coherent scenarios for the creation of a translation system by unguided chemicals” provided by evolutionism/materialism.
    What “coherent scenarios for the creation of a translation system by unguided chemicals” are provided by Creationism/non-materialism/ID? No, the Designer did it! does not constitute a “coherent scenario”—or, if ericB wants to argue that the Designer did it! does constitute a “coherent scenario”, ericB gots some ‘splainin’ to do about how come he doesn’t regard evolution did it! as a “coherent scenario”.
    Myself, I’m okay with the fact that real science doesn’t have all the answers yet. Yes, it would be nice to know how the “translation system” ericB refers to got started in the first place… but if we don’t know, we don’t know. [shrug] C’est la vie, and the fact that real science doesn’t answer one particular Question X does not alter the fact that real science has lots of other answers, for lots of other questions. So yeah, I’ll continue to go with real science, on the grounds of all those other questions real science has answers for. As for ID, well, somebody wake me up when ID has any answers for any questions, okay?

  16. Allan,

    How “the code” evolved from what? A simpler code? No code at all?

    Code, what code?

    Does Alan Fox, the author of the OP, even acknowledge the presence of a code?

    Does Elizabeth Liddle, the host of this blog, even acknowledge the presence of a code?

  17. Is Mike Elzinga a bot? It seems like a bot to me. Same canned response. Next we’ll be hearing about high school and about how Sir Fred Hoyle didn’t understand physics and math.

  18. Mung,

    Sure there’s a code. It’s just not an abstract code. There are no symbols used, no abstract representations anywhere.

    DNA is a code where code means a process whereby the outputs can be mapped to the inputs, nothing more. DNA is a code the same way all chemical reactions are a code.

  19. thorton:

    Sure there’s a code. It’s just not an abstract code.

    What is an “abstract code.” Does it have a mathematical definition?

  20. thorton:

    DNA is a code

    False. DNA is not a code. DNA is a molecule.

    DNA is a code the same way all chemical reactions are a code.

    All chemical reactions are not a code. DNA is not a code.

  21. Yes; it is a bot.

    It is an automatic test for wired-in ignorance. It applies exactly the same stimulus to every ID/creationist and gets exactly the same clueless avoidance response every time.

    It proves, repeatedly that ID/creationists, for all their taunting and self hype, can’t cope with even basic high school science. You failed the test many times; which also means that you don’t even try to learn anything; and that is quite significant.

  22. Mung, you sound confused. Obviously the genetic code and the translation system would have had to evolve, supposing it did evolve, from no code at all. We don’t know how this happened, but there are many different hypotheses on the subject, all of them with elements of testability.

    Again, here’s a video by CDK007 that details one such hypothesis for the code and translation system’s origin from a time around the beginning of life with no code or translation at all:

    So there you have it, that is an in principle explanation for the origin and evolution of the translation system and the genetic code, using known evolutionary mechanisms.

  23. How ‘the code’ evolved from no code at all, though I should hardly have to spell that out. A simpler code (fewer ‘assignments’) being part of the trajectory from there to here.

    As to the rest: why you askin’ me?

  24. It is popularly called a code. But in using that term, people are not making some hard decision about its genesis – calling it something that only intelligent agents can make – but merely recognising that there is a system where one type of configuration – a particular triplet in a reading frame – leads to a different configuration being attached to a growing peptide chain. The relationship is not symbolic, however, but energetic: complementary codon-anticodon pairs bind preferentially, as do the tRNAs specific to a given aaRS. The relationship is more akin to filtration than symbology: from a molecular mess, aaRS’s can ‘select’ their respective substrates, and ribosomes can ‘select’ from that set of products the ones that bind most readily to a given mRNA triplet.

    Shall we now play a game regarding the use of ‘select’ here? Or can we just recognise that we cannot expunge from process descriptions all words carrying some baggage of intent, awareness or agency?

  25. Does Alan Fox, the author of the OP, even acknowledge the presence of a code?

    As we never tire of pointing out, words carry semanic baggage. For an unfortunate example, look no further than “junk” DNA. What we call something is not the defining essence of what it is. I’m perfectly happy to talk about the DNA code. The claim that, because we talk of codes in other contexts, that creates some objective link between things that are otherwise dissimilar is disingenuous.

    ETA:

    Another example is intelligence. We talk of human intelligence, though nobody has yet produced a reliable way of measuring it other than performance testing at specific tasks. And yet there seems a whole philosophy built on extrapolating from this to an amorphous, invisible, undetectable “Intelligence” that can violate the second law of thermodynamics, but only when we’re not looking.

  26. Mung: Next we’ll be hearing about high school and about how Sir Fred Hoyle didn’t understand physics and math.

    No, he did. It’s just biology he had a problem with. I can understand why that might not occour to you however as the denizens of UD seems to believe that they have already proven ID is right without referencing actual biology, only mathematics and physics.

    Odd how few people at UD are actually involved in biology at any level.

  27. A couple quick clarifications for now.

    As I’ve already agreed in posts to Elizabeth (e.g. here) and to others, it would be improper to assume that using words such as “symbolic” in any way automatically implies design by intelligence. Words such as “symbolic”, “code”, and “translation” do appropriately describe the translation system found in all cells, but the question of its origin is a separate one and the focus of the challenge.

    Whatever you might prefer to call it, in any case the translation system in cells is real, and nothing like it is found anywhere else in the universe, other than in the designed artifacts of intelligent agents. Therefore, its origin needs an explanation.

    The nature of the challenge is to see if it is reasonable to infer from the properties of unguided chemicals whether chemicals would construct such a translation system, despite the obvious fact that chemicals have no need for any such system and do completely fulfill all the requirements of the laws of physics and chemistry without any such system. Biology needs information and translation, but chemicals do not need either.

    For the purposes of the challenge, all questions about the chemical feasibility of creating DNA or RNA as a material that could serve as a potential medium are waved. However, particular helpful sequences of nucleotides cannot be merely assumed and would need to be justified, especially in the case of sequences that hold encoded information that must be decoded, i.e. translated according to an organism’s genetic code.

    I hope these clarifications help avoid irrelevant distractions.

    Thanks to all for thinking in a serious way about the origin of the translation system!

  28. ericB: The nature of the challenge is to see if it is reasonable to infer from the properties of unguided chemicals whether chemicals would construct such a translation system, despite the obvious fact that chemicals have no need for any such system and do completely fulfill all the requirements of the laws of physics and chemistry without any such system.

    The challenge itself seems unreasonable.

    We have complex weather systems, maintained by feedbacks within those systems. Nobody expects an explanation of how water and air molecules could construct those weather systems. It is well understood that the complex environment, the heat from the sun, the rotation of the earth, the effects of gravity are all involved.

    For the case of biology, I see it as fairly obvious that complex environments, possibly including energy release from volcanoes, could generate complex systems of self-sustaining chemical reactions. There is still a question of how they could have become sufficiently self-sustaining as to develop the degree of autonomy that we see in biological cells. I’m inclined to think that Lynn Margulis was onto something with her ideas of symbiosis. May two simpler systems were somehow able to form a cooperative union.

    I’ll certainly grant that we have not yet settled the question of the origin of life. We might never settle it. But I don’t see it being as implausible as your description seems to suggest.

  29. ericB,

    Eric,

    Welcome to TSZ. It is refreshing that you are prepared to state upfront that you don’t plan to dive ‘further back’ to the origin of the things from which the code is constructed. It is a frequent derailer of sensible discussion.

    The nature of the challenge is to see if it is reasonable to infer from the properties of unguided chemicals whether chemicals would construct such a translation system, despite the obvious fact that chemicals have no need for any such system and do completely fulfill all the requirements of the laws of physics and chemistry without any such system. Biology needs information and translation, but chemicals do not need either.

    Several issues – the conceptions of ‘unguided chemicals’ and whether biology ‘needs’ translation being the most relevant. Chemical groups interact by following entropic gradients. Any system that can shed energy by reconfiguring will do so. Most of the interactions of biological relevance take place through the electromagnetic force – different atoms have different affinities for electrons. Bringing them in range can result in a redistribution of electrons to allow a lower-energy state to be achieved. This may result in breakage of a bond or its formation, depending on the energetic relationship between start and end.

    The most fundamental interaction in all of biology is the hydrogen bonding between complementary nucleic acid pairs. A pairs with T (or U in RNA) and C pairs with G. One could call this a ‘code’, but it is a physical relationship – to the point that this affinity of pairs is used extensively in forensic and medical procedures – PCR primers and RNA probes work because, presented with billions of bases, they will nonetheless locate and ‘lock onto’ their complementary sequence just a few bases long, with no enzymatic assistance or ‘guidance’ at all beyond electromagnetic interaction and the lower energy of the bound state.

    This complementarity, in tandem with other properties of the nucleic acid bases, has other important implications – single stranded nucleic acid molecules will twist into repeatable shapes, as short stretches of complementary sequence ‘find’ each other, and these can have catalytic activity. Again, nothing is going on other than adoption of ‘lowest-energy’ configurations. Further, complementarity means that a single strand can be prevented from folding in this way – you don’t want everything ‘on’ all the time – by masking the exposed bases with their complement. This is also protective. Again, the prime driver for this is the energetic relation of the complementary sequence. And finally, such a paired molecule can be replicated – the complements can be separated and new complements synthesised (requiring energy), generating two molecules where there was one. This tendency to increase is the most important thing about biology. None of this ‘needs’ translation. The sequence of bases is sufficient to determine how a ribozyme will fold.

    It does not need to, nor does it need to be ‘made’ to. It simply needs … well, it ‘simply’ needs a whole bunch of stuff that they give Nobel Prizes out for solving. Of course I cannot supply any detail (though most of the chemical catalysis required by primitive life can be supplied by very short ribozymes, rendering this possibility at least plausible).

    Of course, I have not even mentioned ‘The Code’ at all. But this principle of complementarity – of preferential binding of complementary sequence – lies at its heart. One end of a tRNA molecule is aminoacylated (by a protein, in the modern system, but ribozymes can do it), and these tRNA molecules are stitched together by a ribozyme, even in the modern system. But no ‘code’ is necessary to make peptide bonds, just this fundamental charge-weld system. Peptides can be made with severely truncated tRNAs just 3 bases long. But this is nonspecific. The peptides made depend on the specificity of the charging system, and the makeup of the acid library.

    There is a gap to be filled here – how does such a nonspecific system of peptide synthesis become a specified one … ie, after a very lengthy post, only now have I come to address your challenge! But if your challenge is simply to present an ‘in-principle’ scenario as to how the multiple components could have come to be, this is it. DNA/RNA are not ‘for’ protein synthesis, but replicatable and catalytic in their own right. Initial peptide synthesis is not ‘for’ making enzymes, nor coded. Complementarity is not ‘for’ repeatably joining amino acids. But they provide the raw materials for the ‘final’ step. Rather than multiple components that have to do their modern job, the components did some other job, but lent themselves to a coding role. Because ultimately, the physical template provided by each triplet provided a handy means of including some tRNAs and excluding others – the first step on the road to tight specificity.

  30. Thanks for the greetings. Here are a few more thoughts that may help avoid some possible misunderstandings and make sure everyone is focused toward the same questions.

    An essential property of a code is that it is an extrinsic association. The association is not an intrinsic property of the medium itself. Consequently, the particular association implemented by a true code could not be determined or derived merely by studying the inherent chemical and physical properties of the medium.

    Allan Miller: “…One way to do this is to use a template, and have the activated amino acids ‘marked’ in some way that binds preferentially with the template. You want to call that symbolic, it’s symbolic. But it isn’t really.”

    I agree; you are correct that template binding is not symbolic. Templates function chemically according to their intrinsic properties. Whenever we have transcription of DNA, the DNA strand functions as a template and the immediate transcript is a predictable reverse complement of the transcribed template sequence. Transcription by itself is never a sufficient indication that anything truly symbolic is happening. From the ENCODE project we are gaining a sense of how the genome is pervasively transcribed, but only a small minority of the genome is “coding DNA” as distinct from transcribing “non-coding DNA”.

    While there are meanings of “information” that can be applied throughout the genome, the hallmark of information that is legitimately “symbolic” is translation via an extrinsic code. That is why I’ve maintained…

    No Translation = Not Symbolic
    or
    No Encoding and No Decoding = Not Symbolic

    Inherent, chemically required associations (e.g. due to direct chemical binding) are never a “code”. This is why every physical medium for symbolic information must be chemically neutral with regard to the content of the message.

    + The chemistry of paper and ink cannot determine what message the paper will hold.
    + The chemistry of slate and chalk cannot determine what message a blackboard will hold.
    + The chemistry of DNA (or RNA) cannot determine the encoded symbolic sequences in coding DNA. If it did, it would become impossible to have the same medium of DNA (or mRNA) carry different sequences.

    There are many ways to see that the genetic code is a true code in which the meaning associated with a sequence is not determined inherently or intrinsically by that sequence. In other words, one could not possibly derive or determine the code only from the chemical properties of the medium of DNA or RNA or of a particular sequence.

    The most direct proof is that there are multiple genetic codes, not only one universal genetic code as was once thought. (NCBI has a web page of “genetic codes.”) For example, a codon that represents STOP (i.e. the end of the sequence) in one organism may instead represent an amino acid in a different organism. For details, please see the examples I gave here.

    GlenDavidson: “Is it at all strange that an evolved information system would be so different from human-produced information systems? Of course nature could never go about being representational, but what works best tends to survive”

    I’m raising a different question in this challenge. The question is not about how similar or different biological systems are from human systems, but rather about whether the chemicals of a pre-biological universe should be expected to ever create any translation system at all.

    BTW, I hope it is clear that when I use the shorthand of “unguided chemicals”, I am not denying the influence of physical and chemical processes. I am simply distinguishing the presence or absence of direction by intelligent agency. I am asking what it is reasonable to expect from “unguided chemicals” behaving according to natural processes without intelligent intervention.

    When I say that chemicals have no “need” for any such translation system, I am simply pointing out that the chemicals of the universe could go on for billions of years, and in fact indefinitely — at all times completely fulfilling all requirements of physical and chemical laws — without ever having such a system for translating to or from symbolic information. Dead rocks and lifeless puddles have no unmet dreams or goals. As far as chemicals are concerned, lifeless chemistry that is completely devoid of any codes, any translation, and any symbolic information can work just fine indefinitely.

    So, why should we think that chemical processes by themselves would produce such an unnecessary system rather than just settle into easy low energy states that don’t have any of those features?

    PLEASE NOTE: An answer to this challenge would shed light on how mindless chemicals with no ability to plan for future function or future benefit could be reasonably expected to navigate the inherent interdependency of the components of any translation system. I illustrated this issue through the example of a DVD player.

    Would the decoding component come before there existed any useful encoded information to decode? What use would that have? That would be like making an operational DVD player in a universe with no suitable DVDs to play.

    Or would the encoded information come before the decoding mechanism? What use would that have? That would be like making accurately encoded DVDs in a universe with no suitable DVD player to decode them. Encoded sequences don’t have the properties of what they represent. It is only through decoding that these can be converted to functionality.

    These are only some of the obstacles inherent in a translation system (e.g. also here). Chemicals don’t care about any of that. They only need to fulfill the laws of nature.

    How then would the operation of the laws of nature, without any guidance from intelligent agency, drive chemicals to the destination of a translation system rather than rest in innumerable other configurations with lower energy? For example, why bother to build anything like a ribosome at all? Lifeless existence without codes and translations is far easier.

  31. Alan Fox:
    As we never tire of pointing out, words carry semanic baggage.

    hahah. Good one Alan. If they didn’t it would be pretty difficult to communicate.

  32. Rumraket:

    Mung, you sound confused.

    Rather I wish to ensure we are all talking about the same thing.

    1. There is in fact a code. No need to use scare quotes, no need to call it by some other name, no need to claims it’s only a code by analogy.

    2. Some people believe the present codes (yes, plural) evolved from one or more “simpler” codes. Some people believe the current codes could not have evolved from a simpler code.

    3. Some people believe that this presumably simpler code somehow arose from no code at all. Other people think the very idea is ludicrous.

    So let’s all just be sure we’re talking about the same thing.

    Allan Miller:

    It is popularly called a code.

    See what I mean? It’s not just “popularly” called a code. It’s called a code by scientists, and for good reason. It meets the mathematical definition of a code. Do you dispute this?

    What is the simplest coding/decoding system you can conceive of? What do you think the present code evolved from?

  33. Hello, ericB! I’m quite willing to concede that “evolutionism/materialism” does not provide any “coherent scenarios for the creation of a translation system by unguided chemicals”. Now, I have a question for you:

    What “coherent scenarios for the creation of a translation system by unguided chemicals” are provided by Creationism/non-materialism/ID?

  34. Mung:

    Mike Elzinga,

    You forgot to mention Hoyle. Silly bot.

    See? The bot got you yet again.

    You read that challenge to do a little high school level calculation; and here you are avoiding it yet again. You still have no clue. You’ll do anything to avoid it.

    It works every time; it has been working consistently for the last 50 years.

  35. Mung:

    It meets the mathematical definition of a code.

    What is the mathematical definition of a code? Can you please provide it as well as your source for the definition. Thanks.

  36. What “coherent scenarios for the creation of a translation system by unguided chemicals” are provided by Creationism/non-materialism/ID?

    Creationism/non-materialism/ID do not propose scenarios for the creation of a translation system by unguided chemicals.

    So to answer your question, none.

  37. lol. really, thorton?

    http://en.wikipedia.org/wiki/Code

    Note, if you will, the reference to symbols.

    If the genetic code is in fact a code, according to the mathematical definition of a code, then it follows that the genetic code is symbolic. Despite uninformed claims to the contrary.

  38. Abstract:

    The genetic information system is segregated, linear and digital. It is astonishing that the technology of information theory and coding theory has been in place in biology for at least 3.850 billion years (Mojzsis, S.J., Kishnamurthy, Arrhenius, G., 1998. Before RNA and after: geological and geochemical constraints on molecular evolution 1-47. In: Gesteland, R.F. (Ed.), The RNA World: The Nature of Modern RNA Suggests a Prebiotic RNA, second ed. Cold Spring Harbor Laboratory Press, Boca Raton, FL). The genetic code performs a mapping between the sequences of the four nucleotides in mRNA to the sequences of the 20 amino acids in protein. It is highly relevant to the origin of life that the genetic code is constructed to confront and solve the problems of communication and recording by the same principles found both in the genetic information system and in modern computer and communication codes. There is nothing in the physico-chemical world that remotely resembles reactions being determined by a sequence and codes between sequences. The existence of a genome and the genetic code divides living organisms from non-living matter. If the historic process of the origin and evolution of life could be followed, it would prove to be a purely chemical process (Wächtershäuser, G., 1997. The origin of life and its methodological challenge. J. Theor. Biol. 187, 483-694). The question is whether this historic process or any reasonable part of it is available to human experiment and reasoning; there is no requirement that Nature’s laws be plausible or even known to mankind. Bohr (Bohr, N., 1933. Light and life. Nature 308, 421-423, 456-459) argued that life is consistent with but undecidable by human reasoning from physics and chemistry. Perhaps scientists will come closer and closer to the riddle of how life emerged on Earth, but, like Zeno’s Achilles, never achieve a complete solution.

    Origin of life on earth and Shannon’s theory of communication.

  39. cubist: Hello, ericB! I’m quite willing to concede that “evolutionism/materialism” does not provide any “coherent scenarios for the creation of a translation system by unguided chemicals”. Now, I have a question for you:

    What “coherent scenarios for the creation of a translation system by unguided chemicals” are provided by Creationism/non-materialism/ID?

    I see Mung beat me to an answer (which may be easy given how intermittently I will be able to post — thanks for your patience everyone).

    All causes could be subdivided into the mutually exclusive categories of
    1. undirected or unguided natural process causes, and
    2. causes involving direction / guidance / design by intelligent agency.

    If it is not reasonable to find the cause for some effect within category one, then the logical inference is that one should reasonably expect the cause to be in category two. (Of course, some play by the rules that this is disallowed as a legitimate option. Therefore, they are locked in by their presuppositions regardless of what evidence and reason indicate.)

    However, we have only started to consider whether or not it is reasonable to find the cause of translation systems in category one. Let’s see what other people can contribute about that, which is the main point of the challenge.

    Thanks for the welcome, and for your question!

  40. Mung:
    lol. really, thorton?

    http://en.wikipedia.org/wiki/Code

    Note, if you will, the reference to symbols.

    If the genetic code is in fact a code, accordingto the mathematical definition of a code, then it follows that the genetic code is symbolic. Despite uninformed claims to the contrary.

    If that is your mathematical definition of ‘code’ then the genetic code does not qualify as there are no symbols involved. A symbol is defined as “A thing that represents or stands for something else, esp. a material object representing something abstract.”

    As I observed before, there is no abstraction involved in the chemical process of DNA being translated to an amino acid. None.

  41. thorton,

    You offer yet again a wonderful example of the incoherence of the anti-ID camp.

    Yockey can’t be trusted. Yet Yockey is “on record as saying he accepts the theory of evolution 100%.” Go figure.

  42. thorton:

    If that is your mathematical definition of ‘code’ then the genetic code does not qualify as there are no symbols involved.

    It’s not my mathematical definition of a code. It’s the accepted scientific definition of a code. Too bad for you and others just like you who choose to deny the facts while asserting you are merely being “skeptical.”

    TSZ is a joke. The only true skeptics here are those who venture here to argue for ID.

  43. 1. Code is defined as communication between an encoder (a “writer” or “speaker”) and a decoder (a “reader” or “listener”) using agreed upon symbols.

    oh crap. there’s that word symbol. reject!

    2. DNA’s definition as a literal code (and not a figurative one) is nearly universal in the entire body of biological literature since the 1960’s.

    reject! reject! reject!

    3. DNA code has much in common with human language and computer languages

    reject! reject! reject!

    4. DNA transcription is an encoding / decoding mechanism isomorphic with Claude Shannon’s 1948 model: The sequence of base pairs is encoded into messenger RNA which is decoded into proteins.

    reject! reject! reject!

    5. Information theory terms and ideas applied to DNA are not metaphorical, but in fact quite literal in every way. In other words, the information theory argument for design is not based on analogy at all. It is direct application of mathematics to DNA, which by definition is a code.

    reject! reject! reject!

    Facts don’t matter.

  44. There is a full version of Yockey’s article available as a free pdf here
    Dunno why anyone would want to wade through the whole thing, but I did. It’s a muddle: part history, part philosophy, part computation of Shannon information, part silly analogies with US zip+5 barcodes … if I do understand the gist of what I read, it’s that we probably cannot, even in principle, arrive at a complete and accurate explanation of how the genetic code evolved. (Cue analogy with Gödel’s incompleteness theorem.)

    But of course, the abstract already said as much.

Leave a Reply