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Semantics and "Specificity"

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  • Semantics and "Specificity"

    The user The Lurch asked for the following exchange to be made public:

    Originally posted by TheLurch
    Originally posted by Seeker
    Originally posted by TheLurch
    Originally posted by Seeker
    Hello The Lurch,

    I have a question you may as a biologist may be able to answer. Dr. Lee Spetner puts forward a notion of specificity in his books Not by Chance and the Evolution Revolution. I want to know if he is just arguing semantics, or if this is a scientifically rebuttable claim. Here is the relevant quote:

    ''Evolutionists accuse me of “dishonestly” changing my definition of specificity to support my statement that no known random mutation adds information to the genome. In their attempt to discredit my book, they resort to calling me dishonest. The reasoning on which they base this smear is nothing but ridiculous. They demonstrate that they do not understand what specificity is, nor do they understand the relationship between specificity and information.

    The specificity of a biochemical reaction reflects the ability of an enzyme to discriminate. The more highly specific, the more highly discriminating it is and the more information it has. The ribitol dehydrogenase (RDH) enzyme has a high activity on ribitol and a low activity on both xylitol and L-arabitol. It is therefore quite specific to ribitol. The mutated RDH has a somewhat lower activity on ribitol and a somewhat higher activity on xylitol and L-arabitol. It therefore discriminates less well than the wild-type (unmutated) RDH between ribitol and the other two molecules. It is therefore less specific and hence contains less information. The mutation has thus reduced the specificity, and therefore the information, in the RDH.

    The streptomycin molecule attaches to the matching site on a pathogenic bacterial ribosome and thereby interferes with its protein synthesis, leading to the death of the pathogen. The matching site discriminates between streptomycin and other molecules, and is therefore specific to streptomycin and this specificity represents information in the matching site. A mutation in the site destroys the match so that the streptomycin cannot attach, granting the pathogen resistance to streptomycin. The mutated site matches to no molecules and thus does not discriminate between streptomycin and other molecules. The mutated site has thus lost its specificity and has lost its information. So this mutation, too, has lost information. The assertion that it becomes more specific because it matches to zero molecules is ridiculous. To say that binding to no molecules has more information than binding to one or two is a joke. My definition of specificity and information is consistent throughout, as opposed to evolutionists (false) charge''.

    https://evolutionnews.org/2016/09/gloves_off_-_r/

    What would be your response?

    Thank you in advance.
    Man, what is it with engineers? I've had it explained to me, but it never ceases to surprise me.

    In any case, i'm happy to answer this publicly, unless you have some reason for wanting it kept private.
    No, go ahead. Just tell me where you will post the response.

    Cheers!
    Go ahead and start a thread, and i'll respond.
    So, I am starting this thread for The Lurch to post his response.

    Thank you!

  • #2
    I just find that there's no predicting what may interest other people, or which explanations might click for some people, even if they're on a topic that has been discussed extensively before. So, i prefer to keep things where other people can see them unless there's reason not to.


    So, there's a number of things in the quoted section. One is equating specificity with information. Two is the issue of defining specificity. And the last is the claim that evolution can't produce information.

    As for issue one, i'm sure it's elaborated more in his book, but all we have here is one sentence: "It is therefore less specific and hence contains less information." What sort of information, and how that relates to specificity is, ironically, unspecified. Information is fundamentally a mathematical concept, and i'm leery of any attempt to leverage it that doesn't seem to involve math.

    In any case, he attempts to relate it to the number of different substrates something can catalyze reactions with. While that's far from the only thing that enzymes do, and thus this is a painfully incomplete view of what evolution is involved with, we'll go with it, because it's at least something that can be looked at in terms of evidence.

    Which brings us to point 2, enzymatic specificity. He talks about these enzymes as if they only have one substrate. But he doesn't know that. Enzymes can typically catalyze reactions with a range of related substrates, limited by chemistry (the bonds have to be very similar) and shape (the molecule has to match the shape/charge of the active site). My expectation is that this enzyme will catalyze reactions with the substrates that were mentioned here, and with a collection of closely related ones - an expectation supported by the fact that both versions already react with at least 3 chemicals. My expectation is that we don't actually know the full range of chemicals that it can catalyze reactions with, because we've only tested a few things that it frequently comes across inside cells.

    That's not the only problem here. Which is more specific? An enzyme that cuts a protein after positively charged amino acids wherever they occur, or an enzyme that cuts after any amino acid, but only works at the two ends of the protein? Those are real examples that exist, and i don't know how to definitively answer that question. And, to return to the example from the quote, this isn't even necessarily an all-or-nothing effect - he wants to rely on complicated things like reaction rates to make these judgements.

    And that's where the apparent lack of math becomes very problematic, because without it, these really do come down to personal judgements, and that's a lousy way to do any science.

    So, to handle point three, let's just accept these questionable claims for now. The argument falls apart the second you start doing transitive logic. If evolution can't produce information, and information is equivalent to specificity, then the claim is that evolution can't produce specificity. And that's just garbage. Let's say that, under certain environmental conditions, one of the three reactions this enzyme catalyzes produces a chemical that's a growth retardant - doesn't kill bacteria, but slows them down considerably. Do you really think that evolution could not possibly produce a version of the enzyme that doesn't catalyze that reaction?

    But we don't need hypotheticals like that; we already know this is wrong. There are cases where two closely related genes produce proteins that bind to different steroid hormones. Their relatedness suggests that they were the product of the duplication of a common ancestral gene. And some researchers looked at the sequence and figured out what the ancestral version probably looked like, and then made the ancestral protein. And, not surprisingly, it could bind to both enzymes. So, the ancestral version became more specific after a duplication.

    And there are many, many examples like this. Teleost fish (the most common type) had a whole-genome duplication early in their history, and have extra copies of many genes now as a result. Humans have 1 version of a signaling protein; fish have two. In fish, the two combined are expressed in a similar set of tissues to the human version, but they're are specific to different subsets of the tissues where the human version is found. To repeat myself, the ancestral version became more specific after a duplication.

    There are countless examples like this - duplication plus evolution changes specificity in countless ways. So, by this guy's own definition, evolution produced information.

    Maybe there's more to his argument in the book, which i haven't read. But if he's accurately summarizing his own argument, then he's not even arguing sematics - he's arguing that a large corpus of evidence doesn't exist.


    Sorry for the verbosity. I didn't set out to pontificate this much.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

    Comment


    • #3
      In my experience it is almost always a red flag when someone starts out with something like "Evolutionists accuse me of..." rather than "Biologists accuse me of..." or "Geneticists accuse me of..." that you are about to hear a bunch of unadulterated claptrap.

      I'm always still in trouble again

      "You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
      "Of course, human life begins at fertilization that’s not the argument." --Tassman

      Comment


      • #4
        I apparently left it too late to edit, so some errata for my extended ramble:

        "While that's far from the only thing that enzymes do, and thus this is a painfully incomplete view of what evolution is involved with..."
        Enzymes should be proteins there, since non-enzyme proteins are also structural, act as channels, influence solution properties, etc.

        "An enzyme that cuts a protein after positively charged amino acids wherever they occur, or an enzyme that cuts after any amino acid, but only works at the two ends of the protein?"
        That should be "one of the two ends". There are protein-digesting enzymes that are specific to the carboxy and the amino ends of proteins, but i'm not aware of any that does both.

        " And, not surprisingly, it could bind to both enzymes."
        Enzymes should be "hormones".

        In the words of newspapers everywhere, i regret the errors (which are always so much easier to spot after a good night's sleep).
        Last edited by TheLurch; 07-08-2019, 08:16 AM.
        "Any sufficiently advanced stupidity is indistinguishable from trolling."

        Comment


        • #5
          Originally posted by rogue06 View Post
          In my experience it is almost always a red flag when someone starts out with something like "Evolutionists accuse me of..." rather than "Biologists accuse me of..." or "Geneticists accuse me of..." that you are about to hear a bunch of unadulterated claptrap.
          In my experience, people who use those phrases are often unaware of existing data that contradict everything they're claiming.
          "Any sufficiently advanced stupidity is indistinguishable from trolling."

          Comment


          • #6
            What do you mean he refers to as "reaction rates"? I can't find the relevante quote.

            Comment


            • #7
              Originally posted by Seeker View Post
              What do you mean he refers to as "reaction rates"? I can't find the relevante quote.
              Here:
              The ribitol dehydrogenase (RDH) enzyme has a high activity on ribitol and a low activity on both xylitol and L-arabitol.
              "Any sufficiently advanced stupidity is indistinguishable from trolling."

              Comment


              • #8
                Thanks.

                Comment


                • #9
                  Specificity was first defined to separate organic chemicals, and organic chemical reactions from inorganic chemical reactions by Baron Jöns Jacob Berzelius. Since then it has been used to describe the specificity of products of chemical reactions mostly in organic chemistry.
                  Glendower: I can call spirits from the vasty deep.
                  Hotspur: Why, so can I, or so can any man;
                  But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

                  go with the flow the river knows . . .

                  Frank

                  I do not know, therefore everything is in pencil.

                  Comment


                  • #10
                    Originally posted by TheLurch View Post
                    What sort of information, and how that relates to specificity is, ironically, unspecified.
                    Don't you think information here is equivalent to complexity?

                    Comment


                    • #11
                      Originally posted by Seeker View Post
                      Don't you think information here is equivalent to complexity?
                      I would say no, complexity in life is a natural product of natural information.
                      Glendower: I can call spirits from the vasty deep.
                      Hotspur: Why, so can I, or so can any man;
                      But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

                      go with the flow the river knows . . .

                      Frank

                      I do not know, therefore everything is in pencil.

                      Comment


                      • #12
                        Originally posted by Seeker View Post
                        Don't you think information here is equivalent to complexity?
                        I would hesitate to put words into the mouth of someone who seems to be speaking incoherently.
                        "Any sufficiently advanced stupidity is indistinguishable from trolling."

                        Comment


                        • #13
                          Originally posted by TheLurch View Post
                          I would hesitate to put words into the mouth of someone who seems to be speaking incoherently.
                          So I take it you regard Spetner's venture as something of a nonsense (or at least parts of it)?

                          Comment


                          • #14
                            Originally posted by Seeker View Post
                            So I take it you regard Spetner's venture as something of a nonsense (or at least parts of it)?
                            Well, i felt my earlier discussion of the issues highlighted some serious problems with it.
                            "Any sufficiently advanced stupidity is indistinguishable from trolling."

                            Comment


                            • #15
                              Originally posted by TheLurch View Post
                              Well, i felt my earlier discussion of the issues highlighted some serious problems with it.
                              You didn't understand what I said. YOU said Spetner's rant was ''inchoerent'', which means you think what he argues is NOT EVEN CLEAR ENOUGH TO REFUTE. Thats why I used the word ''nonsense'' -- which means a meaningless bunch of words.

                              So, I have to ask: do you think the author presents a clear, but wrong, argument, or that we cannot be sure of what he is even arguing?

                              Comment

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