Intelligent Design

Orthomyxo Schools Upright Biped

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Several times now Orthomyxo has sneered at the idea that the genetic code is anything more than “chemical reactions.”  In an exchange with Upright Biped, UB defended the position that the code, while certainly operating through chemical reactions, is just as certainly governed by a staggeringly complex semiotic information system. 

We pick up the debate with UB responding to Ortho by outlining how the system works:

I told you the critical physical condition of the system (described as such in the literature) that allows the system to function as it does, in a material universe determined by inexorable physical law. The gene system must have the physical freedom to specify itseIf, as well as any variation of itself. In case it has not occurred to you, there is no ”capacity to specify” recorded among the physical properties of matter listed on the periodic table, and binding those atoms together does not suddenly create that capacity. It is only established by a particular type of arrangement of matter; one that, as Michael Polanyi noted, “harnesses the laws of inanimate nature” but in an arrangement that is ”irreducible to those laws”. That is exactly what a physical analysis of the system has demonstrated, and is exactly what has been recorded in the literature.

Take out a piece of paper and write the words “DNA codon” at the top of the page. Drop down a few inches below and write the words “mRNA codon”. Drop down further still and write the words “charged tRNA anti-codon”, and below that write the phrase “amino acid presented for binding”. You can now draw a straight line from the top of the page to the bottom, indicating the chain of chemical interactions that begins with a codon of DNA and results in an amino acid being presented for binding during protein synthesis. This would include the processes of transcription, translation and polymerization. But as you will quickly notice, there is no chemical reaction in that chain of events that actually specifies which particular amino acid is being presented for binding.

You can now draw another line (joining your original line, but perpendicular to it) directly underneath the words “charged tRNA anti-codon”. At the end of this new perpendicular line, you can now write the word “aaRS”. The set of aaRS are the molecules in biology that specify which particular amino acids will be associated with each tRNA anticodon. And as I told you before, the work of the aaRS is both temporally and spatially independent of the chain of events represented by the first line you drew down the page. This independence, introduced only by the organization of the system, is what allows the system to function as it does – to specify itself among alternatives. Hence, the word “discontinuous” … as in the discontinuous association between a codon of DNA and the resulting amino acid being presented for biding. It is discontinuous because it has to be in order to function as it does. Check your Periodic Table for that.

What is also worth noting that not a single one of these interactions is even the least bit controversial, which should put your attempted dismissal into proper perspective. But in case it doesn’t, your tacit concession does:

Ortho: “I say if a pool of loaded tRNAs are available then next a/a is determined by the codon, you say the relationship between tRNA and a/a is determined by different chemical reaction. True enough.”

Ortho’s counterargument to all of this was:

I’m sorry ub, but I find this entirely underwhelming

Ouch!  How is UB ever going to overcome such a devastating rejoinder?  Ortho is personally incredulous.  Well, I guess that settles it.  Better luck next time UB.

In all seriousness, Ortho’s antics are embarrassing.  As KF notes, his materialist ideology operates as blinkers preventing him from seeing the obvious information processing aspects of the code.  Just so.  Ortho’s blinkers have, once again, caused him to step into the hole of inanity. 

32 Replies to “Orthomyxo Schools Upright Biped

  1. 1
    jawa says:

    Could it be that UB’s interlocutor meant that UB’s explanation is “entirely underwhelming” because it’s an oversimplification of the actual processing of complex functionally-specified information that is observed in the biological systems?
    🙂

  2. 2
    ET says:

    Ortho thinks that proof-reading, error-correction, editing and splicing can all occur without knowledge. Unfortunately Ortho never provided anything to support that claim. Everything we know about proof-reading, error-correction, editing and splicing says they all require knowledge to complete.

  3. 3
    Bob O'H says:

    Ortho’s counterargument to all of this was:

    I’m sorry ub, but I find this entirely underwhelming

    Orthomyxo’s complete response was that this was “entirely underwhelming with regards to Barry’s original claim”. Has someone been keeping score well enough to be able to quote Barry’s original claim? I’ve gone back through 5 pages of posts and I’m not sure if I’ve found it.

  4. 4
    ET says:

    The claim was in regards to whether or not the genetic code works via chemical reactions. Ortho and Eddie think that it does. Although they seem to ignore all evidence against their claim.

  5. 5
    ET says:

    Barry had asked:

    “Are you suggesting that the genetic code works through a series of chemical reactions?”

  6. 6
    Ed George says:

    Bob

    Has someone been keeping score well enough to be able to quote Barry’s original claim?

    It was this: “Are you suggesting that the genetic code works through a series of chemical reactions?” And nobody in that thread could explain how it didn’t work through a series of chemical reactions. All they did was talk about codes and origin of DNA, neither of which was relevant to the original question.

  7. 7
    martin_r says:

    ET @2

    i am a mechanical engineer… years ago i started to look closer at all the ‘evidence’ supporting the Darwinian theory of evolution… i still do a lot of study (mainstream papers).

    When i first learned about DNA proofreading and repair, i thought that these Darwinian clowns must be joking, claiming, that this was created by some non-intelligent, unguided process… by some hit-and-miss, trial-and-error process… Darwinian clowns must be perverted in some way …

    I think that DNA proofreading/repair is an ultimate proof of designed life, an undeniable proof.
    Of course, when you are mentally ill, you can deny anything…

  8. 8
    Fasteddious says:

    In different ways, both views are correct. Just as a laptop computer is “only” physics in operation (mechanical motions, magnetic fields, electric fields, electron and photon movements, etc.), so too are the DNA – RNA – Protein operations in the cell “only” chemistry in action (molecular bonds, transference of electrons, attractions & repulsions, catalysed reactions, etc.). Yet without the codes introduced into the physics, nothing meaningful happens in the computer, and without the codes inherent in the DNA, nothing meaningful will happen in the cell.
    The key word, of course, is “meaningful”. The meaning in a computer is contained in the codes used by humans to control and provide purpose and direction to the computer operations. Similarly, the “meaning” in a cell comes about as the cell metabolizes, moves, grows, generates products, and reproduces, all for its own purposes and functions.
    The physics and chemistry are necessary and essential to the meaningful processes, but without the codes that determine what the chemistry and physics will do, there is no meaning, purpose, or higher level functionality.

  9. 9
    martin_r says:

    Is DNA a code?

    $10M OOL PRIZE Perry Marshall debated this issue years ago…

    here is the summary:

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

    – 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.

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

    – 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.

    – 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.

    Look here if you look for more detailed arguments:

    https://evo2.org/dna-atheists/dna-code/

  10. 10

    .
    #6

    Yes, that’s Ed’s cop out.

    You can even show him that the “series of chemical reactions” that begins with a codon of DNA and ends with an amino acid being presented for binding does not establish the genetic code. You can show him it requires a particular organization instead, and why it must be that way.

    But he is a man determined to protect his religion from science. So he won’t attack or deny the facts, he’ll just cop out on the phrase of the question.

    Too easy.

  11. 11
    ET says:

    LoL! @ Ed George:

    And nobody in that thread could explain how it didn’t work through a series of chemical reactions.

    Ed wants us to prove a negative. Ed ignores mRNA processing, proof-reading and error-correction.

  12. 12
    orthomyxo says:

    the code, while certainly operating through chemical reactions

    I’m sorry, are you suggesting the genetic code works through a series of chemical reactions!

  13. 13

    .
    Wow.

    Age regression.. Grade school.

  14. 14

    .
    Ortho,

    Since you got the establishment of the code wrong, perhaps you’d like to try again:

    As you now know, the set of aaRS are the molecular constraints in the cell that establish the genetic code. They are fundamentally required for the gene system to begin to function. They are also complex proteins which are synthesized inside the cell from memory, and it is undeniable that there was once a time when no aaRS had ever been synthesized.

    At the point in earth’s history when the first ever aaRS was synthesized from memory, how many of the other aaRS had to be in place?

  15. 15
    Heartlander says:

    Brian Miller summarizes the minimal requirements for life
    :

    Cellular biologists have attempted to identify the minimally complex genome: the minimal number of genes and proteins that would be required for the simplest viable cell. Independently, engineers, computer programmers, and mathematicians have attempted to identify the minimal components required for a machine to make a fully functional copy of itself (i.e., self-replicate). The results from these separate studies have converged to identify components that must have existed at life’s origin (here, here, here), which include the following:

    Large repositories of information and information processing.
    Manufacturing centers that construct all of the essential pieces.
    Assembly and installation processes for all components.
    Energy production and distribution machinery.
    Automated repair and replacement of parts.
    A boundary with control gates that allow specific materials in and out.
    Global communication and coordination with feedback control systems.
    Sensing of environment and calculation of needed responses.
    Self-replication, which draws upon nearly all other essential functions.

    These minimal requirements entail several hundred enzymes and over a million bits of information. That amount is roughly equivalent to the information contained in Charles Dickens’s A Christmas Carol

  16. 16

    .
    What does logic and physics tell you Ortho?

    Shall we squint our eyes and hope for the best?

  17. 17

    .
    Shall we wave our hands at the “difficulty” of the question and just say nobody knows ?

  18. 18
    kairosfocus says:

    Folks, if a sampler of interwoven code — HT, Wiki . . . !!! — will not make a difference to such minds, nothing will. And it patently doesn’t. That is telling, given the level of sophistication implicit in such interweaving. KF

  19. 19
    Seversky says:

    Martin_r 9

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

    Okay, so much like a language. In that case, who is the “writer” or “speaker” or “author” of the code who uses it to transmit meaningful information and who is the “reader” or “listener” who extracts meaningful information from it?

  20. 20

    .
    Sev, there is not a little designer in your computer reading the code that your keyboard’s internal processor sends to the keyboard controller attached got your CPU. Did you think think there would have to be one if the programs running on your computer are written in a language, like machine code for instance.?

    Have you ever heard of that term?

    – – – – – – – – – – – – – – – –

    EDIT: Sev, we know how to make an arrangement of matter read and understand a string of symbols instantiated in another arrangement of matter, which we often call call a medium or media, or memory. Smart people figured it out. These systems require one arrangement of matter to serve as a symbol vehicle, and another arrangement of matter to establish what is being specified – just as Charles Peirce said it would 160 years ago; just as Alan Turing exemplified with his table of transformations; just as von Neumann predicted in his theory of automata; and just as Francis Crick theorized in his adapter hypothesis in genetic translation (which was confirmed, along with von Neumann).

  21. 21
    Ed George says:

    KF

    Folks, if a sampler of interwoven code — HT, Wiki . . . !!! — will not make a difference to such minds, nothing will.

    So, you are claiming that DNA doesn’t work through a series of chemical reactions. Why don’t you or UB, or BA submit a paper for publication on the non-chemical formation of proteins? A Nobel prize awaits you.

  22. 22

    .
    Oh I get it Ed, you’re going to invent something no one says, and then mock it like a child — all to save you from having to stomach the actual science, and history of science, that no one has even the slightest question of.

    Powerful stuff, Ed. A cop out In a class all by itself.

  23. 23
    martin_r says:

    Seversky @19 “who is the “writer” or “speaker” or “author” of the code “and who is the “reader” or “listener”

    i will answer your question, when you finally answer my question (i already asked it like 1000x).

    WHAT IS YOUR EDUCATION ????

    It is important to know, otherwise, i am not sure i can comprehensively answer the question about the ‘speaker/ listener’…

    PS: it is clear that you will never answer my question about your education, so i suggest, you read the whole “IS DNA A CODE?”-debate on Perry Marshall page (Perry is the main person behind the $10M OOL PRIZE) . There you will find many questions from people like you (Darwinian clowns), and Perry will answer all of it using quotes and definition from mainstream science papers and books. Perry Marshall did a perfect job in fighting Darwinian clowns who infested the whole world with their crazy absurd theory. Seversky, go and get it, but i am not sure that your mental capacity is big enough to get all Perry Marshall’s arguments … Seversky, once again, whatever question (in regards to DNA code) you have, Perry Marshall already answered it here: https://evo2.org/dna-atheists/dna-code/

    a small sample from the debate:

    Q (A Darwinian clown asks): DNA is subject to random mutation. What intelligently created code experiences random mutation?

    A (Perry Marshall answers): All communication systems are subject to mutations, following the laws of probability. That’s why Ethernet and TCP/IP have error correction and redundancy features. DNA has error correction and redundancy features as well. Note that mutation, noise and entropy are all the exact same thing in communication theory – and they are all undesirable.

  24. 24
    kairosfocus says:

    EG, I duly note your insistent strawman caricature and refusal to engage the layer cake architecture of information and communication systems. Beyond a certain point repeated mischaracterisations such as you indulged yet again become willful disregard to truth and an implicit recognition that the truth is your enemy. You will not not acknowledge manifest truth here, despite repeated correction and opportunity for a rather obvious reason, it does not fit your ideological agenda. Where, truth says of what is that it is and of what is not that it is not, accurate description of reality. Enmity to manifest truth is a war against reality, which will fail in the end but often after horrific needless cost. Sad, but now we must begin to draw and act on prudent conclusions. Here, it is manifest that D/RNA is alphanumeric code working through molecular nanotech that uses chaining polymerisation and the physics of H-bonding etc. Where, we have clear cases of interwoven code, exponentially harder to do than already FSCO/I rich coding. We even have position arm devices and mini assembly line transfer machines, with edited control tapes using Yale lock like prong height coding. These have been known for decades, and so we must reckon with a mortally wounded paradigm trying to hold on to its power base even as it bleeds out. Rather similar to the old USSR. KF

  25. 25
    kairosfocus says:

    MR, the interlocutor is ignorant of noise and entropy? KF

    PS: PM does a great job, I see both Shannon and Yockey.

  26. 26
    ET says:

    Ed George:

    Why don’t you or UB, or BA submit a paper for publication on the non-chemical formation of proteins?

    Nice strawman. Does it make you feel good to make crap up as if your opponents said it and attack it?

    What is the chemical reaction directing proof-reading and error-correction? Is the use of chaperones to help the protein fold into its functional configuration, just a chemical reaction? Can you map out that reaction for us?

  27. 27
    jawa says:

    UB @14:

    “ At the point in earth’s history when the first ever aaRS was synthesized from memory, how many of the other aaRS had to be in place?”

    How was the first aaRS synthesized?

    🙂

  28. 28
    Seversky says:

    Martin_r 23

    Perry Marshall did a perfect job in fighting Darwinian clowns who infested the whole world with their crazy absurd theory. Seversky, go and get it, but i am not sure that your mental capacity is big enough to get all Perry Marshall’s arguments … Seversky, once again, whatever question (in regards to DNA code) you have, Perry Marshall already answered it here: https://evo2.org/dna-atheists/dna-code/

    Quoting a former marketing consultant as an expert on evolution and the genetic code is about par for the course for ID/creationism. I’ll grant he sounds pretty glib – which I would expect given his background – but it’s easy to win an argument if you’re running both sides of it, as was noted before.

    If you and UB are interested in an entirely different perspective then you could look here:

    Genes – the language of God 4: Why genes aren’t a language

    In passing, he touches on the elephant on the room of this debate:

    One advantage, shared also in calling genes information, is that it sets up a “problem” that can be “solved” by divine action or intention. For example, one of the main kinds of advocates for genes as linguistic things is the intelligent design movement. If genes are meaningful, or the result of some intent, then that implies that one needs to have a deity (or something very like it) to give that meaning. If genes are not informational or linguistic things, though, but at best only something that can be analogised to language, then that “solution” is no solution at all.

    Now, please deny that all this is about the genetic code being a language and, hence, evidence for your God.

  29. 29
    ET says:

    seversky is so pathetic. It doesn’t realize that if his position actually had something then they would be able to refute the words of a former marketing consultant. Yet all they can do is point out that he was a former marketing consultant.

    The real elephant in the room is the fact that neither seversky nor any other a/mat can present any evidence nor science to support their claims.

  30. 30

    .
    Seversky,

    Please do tell us — exactly what part of the page you linked to has any effect on the actual science recorded in the literature?

    Is it the factually dubious part, or the strawman part, or the part that the author admits doesn’t actually have any effect on the question?

    Can you actually name it, Sev? Can you say what it is? Can you say how it changes the physical analysis?

  31. 31
    jawa says:

    UB,

    Do you think your objecting interlocutors here could help with answering the question @27?

    🙂

  32. 32
    martin_r says:

    Seversky @28

    first of all, WHAT IS YOUR EDUCATION ???? WILL YOU FINALLY ANSWER MY QUESTION ???
    I debated lots of Darwinian clowns like you, and you are not the first one who hesitated to answer this question (despite i have asked repeatedly…)

    However, let me correct you, because as per usual, you Darwinian clowns got it all wrong again.

    Perry Marshall is an electrical engineer, and, an IT expert …. AND THEN, a marketing expert.

    Moreover, and this might surprise you, he is the author of the following book:

    “Industrial Ethernet”
    https://www.amazon.com/Industrial-Ethernet-Third-Perry-Marshall/dp/1945541040

    Seversky, did you ever hear the word “ETHERNET” or “TCP/IP Protocol” ?

    So tell me Seversky, who is more qualified to talk about codes/encoding/decoding ?

    An electrical engineer/IT Expert/An author of a book on Ethernet

    or

    a biologist ?

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