A (repeated) challenge to Upright Biped

Upright Biped,

Before fleeing the discussion in July, you spent months here at TSZ discussing your “Semiotic Theory of ID”. During that time we all struggled with your vague prose, and you were repeatedly asked to clarify your argument and explain its connection to ID. I even summarized your argument no less than three times (!) and asked you to either confirm that my summary was accurate or to amend it accordingly. You failed to do so, and you also repeatedly refused to answer relevant, straightforward questions from other commenters here.

Here is my most recent attempt at a summary of your argument, from July 22nd:

X1. All irreducibly complex systems are designed.
X2. All semiotic systems are irreducibly complex.
X3. Therefore, all semiotic systems are designed.

Y1. A system involving representation(s) and protocol(s) is a semiotic system.
Y2. Protein synthesis involves a representation and a protocol.
Y3. Therefore, protein synthesis is a semiotic system.

Z1. All semiotic systems are designed (by X3).
Z2. Protein synthesis is a semiotic system (by Y3).
Z3. Therefore, the protein synthesis system is designed.

If you think this is an accurate summary, then tell us. If you don’t, then please make corrections while maintaining the explicit and concise format of the summary.

I reiterate the challenge, with special emphasis on the bolded part above. Note that since you claim that your argument is an argument for ID, it must lead to conclusion Z3 or something similar:

Z3. Therefore, the protein synthesis system is designed.

If it does not, then it fails as an argument for ID.

Also worth repeating are some observations I made earlier regarding your evasions:

Upright doesn’t realize how obvious his predicament is to the rest of us.

Suppose he had a strong argument (or at least thought that he did). Then he would have every reason to make his position clear and to answer questions forthrightly, secure in the knowledge that his argument would stand up to scrutiny and criticism. On the other hand, he would have no reason to evade or obfuscate, as doing so would only create the impression that his position was weak.

Now suppose that his argument is weak, and that Upright knows this. Clarifying his position in this case would be disastrous, as it would lay bare the flaws in his argument and render it vulnerable to decisive refutation. Evasion looks weak, but at least it allows him to pretend that his argument is strong and that the only problem is that people have failed to understand it properly.

So far Upright’s behavior matches the second scenario perfectly. We thus have every reason to believe that Upright’s argument is weak and that he knows it.

You can choose to evade and obfuscate, Upright, but be advised that we know exactly why you do it.

I invite you to prove me wrong. Either confirm that my summary above is correct, or amend it while maintaining its explicit and concise format so that it accurately represents your argument.

Clarify or evade. It’s your choice.

340 thoughts on “A (repeated) challenge to Upright Biped

  1. Lucky for us that gpuccio did NOT ignore this teeny problem!

    I hope Mung gives credit to at least gpuccio for showing another flaw in UB’s logic.

     

  2. Mung’s argument appears to be summed up by: “Design in Nature. Isn’t it obvious?”. So he can certainly never be refuted. Obvious is … obvious. To those to whom it is obvious.

    I’m still waiting for a serious response to my suggestion, that the modern system of multiple assignments is entirely plausibly derived from a limited library of few or one assignment, perhaps with no protein at all in the early system, certainly none made by this means, but with gradual incorporation as catalytic proteins began to be made by it.

    The only answer offered – you can’t synthesise protein without protein (or rather, “a limited system would not have the information carrying capacity to be a system”) is, frankly, hopeless. The feeble turnaround – build such a system then, else ID (somehow) wins (despite not being the ‘default’) – is thoroughly unconvincing. A logical possibility is not accepted unless one can show it to be a physical possibility! Since peptidyl transferase – the core function – is catalysed by RNA, the only uncertainty is in charging tRNA. And there is no reason to suppose that to be beyond RNA’s catalytic capacity. 

    Keeping denial up for 549 posts, and 100 times that number, is, of course, a doddle. Just keep saying the same things, pour scorn on all objectors and repeatedly declare victory.

  3. As many of you have noted, Upright Biped’s argument fails to reach a conclusion of design. For example, the latest UD version of the argument leads to this tepid and underwhelming conclusion:

    CONCLUSION: These two physical objects (the representation and protocol) along with the required preservation of the arbitrary component of the representation, and the production of unambiguous function from that arbitrary component, confirm that the transfer of recorded information in the genome is just like any other form of recorded information. It’s an arbitrary relationship instantiated in matter.

    The obvious response is “So what? What does this have to do with ID?”. Yet every time someone asks him, Upright Biped refuses to explain how his “semiotic argument” is an argument for ID.

    It’s a very odd thing when an ID proponent — who is flogging his “Semiotic Theory of ID”, on a pro-ID blog no less — refuses to explain how his argument has anything to do with ID. It made me suspicious, so I did a little Googling.

    I found a thread at politicalbuddies.com where Upright shows up and offers to present his argument. He posts the usual screed to Larry Moran following this hilarious rewrite of history:

    This second post is an argument I made to the Professor of Biochemistry at the University of Toronto, Dr Larry Moran; a very hardened materialist whom treasures any chance to beat his opponents down with his superior intellect. After all, he has eight collegiate-level textbooks on biochemistry to his credit. His response was direct – he immediately evacuated himself the conversation. The same argument was presented to biologist and NCSE operative Nick Matzke. His response was just as direct, he immediately refused to engage the evidence, and tried repeatedly to change the conversation. Also in the chain was Dr Elizabeth Liddle, a Neuro-Scientist in the UK. She debated the topic for a period of several months, only to eventually retract her original claim (she claimed she could simulate the rise of recorded information like that in DNA), and cease responding to the debate. Also there was Dr Robert Collins at the Department of Molecular Biophysics at Yale, who presented no contrary evidence, and ultimately, simply said anything in order to have anything to say. Others have given the same general response.

    But here’s the really interesting part. A commenter asks:

    if u could some all this raz up uprightbiped in one or 2 lines, what would u say?

    Believe it or not, Upright actually responds with a condensed summary of his argument:

    Firstly I wouldn’t attempt to. I am not sure what principle is at work which suggests that multi-faceted subjects must be explained in two sentences. Some things appropriately require a thoughtful engagement. But if forced, I would say:

    There is no empirical evidence of any kind whatsover (or even a plausible conceptualization) that chemicals have the capacity to create symbolic representations of other chemicals, nor establish the protocols fundamentally required for those symbolic representations to be decoded back into an effect. When Francis Crick discoverd the code within DNA he referred to it a as “frozen accident”, and then later suggested that perhaps space aliens set the code. In the 50 years since then, there has been zero advancement of a material explanation.

    That’s it, folks. The Great Semiotic Theory of ID, which Upright says he’s been working on since 2009, is nothing more than the hackneyed ID Argument from Incredulity. Upright doesn’t see how it could have happened. Therefore the Designer did it.

  4. Submitted on 2012/09/18 at 6:14 pm (by  Alan Fox on behalf of Onlooker)

    Hello,

     

    kairosfocus is demonstrating his respect for open discussion by banning me from his threads at UD.  Apparently pointing out his hypocrisy and intellectual cowardice is grounds for him to demonstrate, well, hypocrisy and intellectual cowardice.

     

    In any case, if gpuccio is reading here or if anyone can still post in this thread, here’s what I wrote:

     

    gpuccio,

     

    Are your concepts of functional complexity and dFSCI intended to be used to identify design where it is not known to have taken place or merely to tag design where it is known to have happened?

     

    Obviously the first option.

     

    In that case, I think you have a fundamental problem because you are defining dFSCI such that only “non-deterministic” mechanisms can create it. Just so I’m clear, do you consider evolution (random mutations of various types, differential reproductive success, neutral drift, etc.) to be deterministic? If so, dFSCI doesn’t distinguish between “designed” and “non-designed” but between “known to be designed”, “known not to be designed”, and “unknown”. And just to be further painfully clear, would you agree that deterministic mechanisms can create functional complexity of more than 500 bits, by your definition?  

     

    Thanks,

     

    onlooker

  5. Which, as I’ve argued from the earliest engagement with UPB, adds no value to Crick’s original analysis. Other than the absolute lie that nothing has been learned in the last 50 years.

    He, of course, hedges by saying we don’t have a detailed scenario.

    Imagine that. 50 years and we haven’t cracked a four billion year old cold case. Sherlock concludes it was magic.

  6. Perhaps it’s time to start a fresh thread in which UPB is invited to provide a rigorous proof that a semiotic system cannot evolve from a simple replicator. Perhaps he can address the generic subject of signalling systems.

  7. There is no empirical evidence of any kind whatsover (or even a plausible conceptualization) that chemicals have the capacity to create symbolic representations of other chemicals, nor establish the protocols fundamentally required for those symbolic representations to be decoded back into an effect. 

    Once more unto the breach! Three physical DNA bases are not a ‘symbolic’ representation of an amino acid. It really is that simple. In certain circumstances, a particular triplet of DNA bases may be involved in a causal molecular chain that results in a particular amino acid getting stuck on the end of a peptide chain. Equally, it may participate in regulator binding, or be edited out of mRNA, or cause nothing more than its complement to be added during DNA replication (which as a minimum all bases do, wherever they sit).

    It’s like saying that a wax impression of one face of a coin (which could be used to forge its counterpart) symbolises the design on the flipside, simply because of a regularity in physical association observed with coins currently in circulation. Today, there are 20 ‘heads’ and up to 61 ‘tails’. If you know ‘tails’, observation gives you an excellent chance of deducing ‘heads’. What does that tell us about the past? In itself, bugger all.

    When Francis Crick discoverd the code within DNA he referred to it a as “frozen accident”, and then later suggested that perhaps space aliens set the code. In the 50 years since then, there has been zero advancement of a material explanation.

    Au contraire. The literature is vast. It is admittedly of a speculative nature, since we have no exemplars of non-‘coding’ life, but the discovery that the core peptidyl transferase reaction is RNA-catalysed – only about a dozen years ago – was highly significant. If it had been protein-catalysed, this would still not rule out RNA precursors, but anyway it isn’t, so that strengthens the case for RNA. Other lines of evidence on an evolutionary scenario relate to the familial sequences and catalytic mechanisms of aaRSs and tRNAs, and of amino acid biosynthesis pathways, and their chemical property distribution across the codon matrix; the late arrival of aaRSs in the tree of proteins of their class; the frequent absence of direct anticodon involvement in aaRS-tRNA binding, the relative ages of ribosomal subunits and the parts of tRNA with which they interact, the pattern of ‘non-universal’ elements of the code and their curious clustering around STARTs and STOPs; the many known non-catalytic functions of protein, which even a ‘primitive’ peptide synthesis machinery could serve … I trust that Biped’s formal write-up will include, in best scientific tradition, a fair and accurate summary of the present state of knowledge and opinion within the field on the matter, rather than the final sentence quoted.

  8. Joe: “Please demonstrate that a non-material designer, can record transferable information without utilizing an arrangement of matter in order to represent that information, IN THIS MATERIAL UNIVERSE. “

    Joe, how does the information leave the “non-material designer” if there is no “matter” in the “non-material designer” himself?

    We have “information” in a “designer” who himself is NOT composed of matter.

    Where is the “information” residing in the designer if there is no “matter”?

    If there is no “matter”, how is that first “information” transferred across the boundary between the “non-material” designer and the “unrecorded” matter waiting for the “information”?

    A “non-material designer” would be evidence that matter is NOT required for UB’s “transfer of recorded information”.

     

  9. Joe: “Please demonstrate that a non-material designer, can record transferable information without utilizing an arrangement of matter in order to represent that information, IN THIS MATERIAL UNIVERSE. “

    But Joe, that is YOUR side’s argument!   🙂

    gpuccio: ” Now, I will happily admit that the designer needs to manipulate matter to design biological information. And yet, if we exclude the hypothesis of aliens, I will also admit that the most likely scenario for the biological designer(s) is that he is not a physical being with a body. So, what about that?”

    Toronto: It means that you’ve just said that Upright BiPed’s claim that “information transfer” requires an “instantiation of matter” is false.

    Do you follow Joe?

    We have a “non-material designer”, a designer who is NOT instantiated in matter, but nevertheless, contains “information” that needs to be transferred TO matter.

    In order to “transfer information”, he CANNOT use matter since he is NOT composed of matter.

    This means UB’s claim of a “protocol” instantiated in matter is also NOT required and also NOT possible since the sending end, the “non-material designer” has no matter in his being where the “information” is stored.

  10. Apparently with magic, you can be material and non-material at the same time.

    Perhaps Barry will put up one of his gotcha threads to resolve this, 

  11. Joe: “That doesn’t follow. A non-material designer can/ would still use the matter and energy in this material universe to transfer non-material information in this material universe. “

    He could only do that if UB is wrong.

    e.g.  [non-matter(non-material designer)]—-> [matter(biological object)]

    *How* could a “non-material designer” do this?

    If the methods are “non-natural”, you are talking of “biblical creationism”.

     

  12. Since it is the hope of most of the ID side that their consciousness should survive death (I wouldn’t mind it myself, to be honest, provided it is not too much of a ‘monkey’s paw’ gift, though I’m probably ineligible anyway …), I’m surprised that the ‘material instantiation’ part of UB’s thesis does not get more of a theological roasting from his own side.

    I’m not really sure why UB insists so much that info transfer be instantiated in matter anyway. There could (logically) be a variety of ‘semiotic’ systems, some with a material basis (all boiling down to transfer of photons, which are the real info-carriers in chemistry and nervous systems, as well as eyeballs) and some not.

  13. Joe: “By reconfiguring the matter and energy in this material universe, duh. “

    Then the designer “bypasses” “the laws of physics.”

    If ID requires that the “laws of physics” don’t apply to the “designer” and his relationship with his “lifeforms”, then the designer is implied to be “God” and therefore, ID should NOT be taught in schools.

    You haven’t made a case Joe, that ID should be taught outside of Sunday School.

    kairosfocus won’t like what you’re saying here and neither will UB.

  14. This statement by UB over at UD is sure to break all irony meters.

    Jerad,

    You say OoL is important, but you don’t want to discuss it.

    You say you don’t understand OoL issues and don’t like chemistry, but you ignore a conversation centered on OoL which requires only a clear mind and a few technical points – each of which can easily be verified within one sitting at a Google search engine.

    I think you’ve set up a deliberate cocoon.

    One of the common characteristics of ID/creationism apologetics on the internet seems for its proponents to remain completely and willfully ignorant of basic chemistry and physics. It’s the logic of young children; if you don’t turn your head to look at it, it doesn’t exist, therefore it needs no consideration.

    This “semiotic” theory concoction is simply another attempt to make ID/creationism look “sophisticated” by the use of pseudo-philosophical argumentation. It is the use of long, obscure sentences, comprised of rubber words and vague subject/object references, with made-up definitions and unconventional meanings. The idea seems to be that if the sentences are extremely long and full of big words with vague meanings, it must be deep philosophy. The further implication is that those who seek clarification are simply too intellectually inferior to grasp deep thought.

    Again, it is only a cargo cult imitation of knowledge they don’t possess; and watching that KF character is like watching a goofy witch doctor, dressed up in garish face masks and feathers, dancing around, yelling, and trying to scare people. It would be really funny if it weren’t so pathetic.

    Up until the last year or so, I didn’t pay all that much attention to UD; after a few reads, it was just too boring. But after I noticed the brutal banning of Elizabeth and the others here, I looked at some of the characters over there more closely. It appears that ID/creationist apologetics has taken on most of the characteristics of the Spanish Inquisition in the way it deals with questioners. One is also reminded of how Michael Servetus was dealt with by John Calvin.

  15. I want to be conversant with the recent research and thinking along the lines of the RNA-world hypothesis (among others). I simply haven’t taken the time to do so as of yet. I wouldn’t consider my opinion on the matter as being valuable or worth listening to. I’d just be offering dogmatic talking points which I do not want to do.

    This just drips with sarcasm.

  16. I wasn’t following the thread, but I think KF had previously banished onlooker from threads he started. Since KF is not a mod, and since I made the Undesirable Number One list for suggesting that KF has any influence over moderators, let me reassure everyone that KF is not a mod and only abuses mod powers on his own threads.

    It is a nice laboratory demonstration of what debate would be like if he managed the whole site. One could imagine that he might set up entire threads as traps to rationalize banning of troublesome posters.

    Just kidding. KF isn’t that much of a jerk.

  17.  

    gpuccioSeptember 19, 2012 at 1:04 pm

    LarTanner:

    I can’t say that all things we could viably consider codes necessarily presuppose an author figure–a conscious, tool-using being. I can’t say this because I don’t know.

    Well, I am not aware of any example of symbolic code naturally arising without any conscious design.

    http://www.uncommondescent.com/design-inference/it-seems-that-tsz-objector-to-design-af-insists-on-the-long-since-corrected-canard-that-design-is-a-default-inference/#comment-433806

    This leads me to think of my early programming days in which I worked in  COBOL shop where close to a thousand programmers and analysts worked every day making niggly changes to an existing system whose origination was mythical.

    Gpuccio, observing that nothing but Lenski-like changes are being made by programmers, would conclude that the system could not have been originated by programmers. Programmers have only been observed doing micro-programming. It is inconceivable that this process could have done macro-programming (pun not intended).

    The inference that an observed process has less status than a never observed magic sky fairy is so mind boggling insane, that I simply can’t it being made by an honest thinker. Sorry, Elizabeth, but this breaks my will to credit good faith.

  18. Joe : “Do we also “bypass” “the laws of physics”? “

    No and that is THE point.

    We, meaning you and I, are material, and thus, do what UB says we have to do, and that is use “matter”.

    Your designer is “immaterial”, and is NOT bound by physics.

    And that means…., he does NOT use “an instantiation of matter”, to transfer information.

    That means that according to you, an “instantiation of matter” is NOT required to transfer “information” into the material world.

    UB won’t like that.

     

     

  19. On the contrary, intelligent search can create some complex functional information. A very good example is bottom up protein engineering, which is based on:

    a) A previous definition and understanding of the function that has to be found.

    b) Targeted variation, possibly applied to selected starting sequences.

    c) Intelligent selection of the results at each step, based on direct measurement of the function one wants to develop, even at very low and practically ineffective levels.

    That kind of algorithm can, patiently, generate functional information. And it is a deterministic algorithm that uses some random variation. But, as you can see, the function is predefined in the algorithm, and all the parts of the algorithm are deviced intelligently to measure and develop that function.

    IOWs, the situation is similar to that of the pi generating software.

    That illustartes well the power of intelligent design.

    Then perhaps Axe or someone could demonstrate the power of intelligent selection by re-doing the Lenski experiment using intelligent selection. It should go much faster.

    HAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHA

    Oh man, laughing that much makes my sides hurt.

  20. Did I omit a key piece of the challenge?

    Your designer gets the functional specs and has to figure out from the function how to derive the code. No fair looking at what happpened in the Lenski experiment.

  21. Joe: “You alone provide ample reason why IDists should not post on TSZ. “

    IDists should post *everywhere* so that *everyone* can see how badly thought out their arguments are.

    For instance, onlookers have seen you fail at explaining the “immaterial/material” junction.

    How does “information” get transferred if one side has no matter available?

    It’s clear you don’t have an explanation, even a weak one.

    They see you fail, we pick up a point! 🙂

     

  22. Joe isn’t even clever enough to read the analysis of the Lenski experiment and realize that no one knows what the first enabling mutations were or why they were necessary. Even after the experiment is over. So how would the designer intelligently select them?

    Intellignt selection fails even within the bounds of Behe’s Edge.

    The reason bacterial evolution works is that even beaker sized populations are numerous enough to exhaust all possible variations, and have enough time left to do some genomic handstands.

    But don’t trust me. Read gpuccio’s desctiption of how a designer would work, selecting specific variants at each step.

    Step back and let GP explain how he would intelligently select the enabling mutations in the first step and how he would speed things up over blind fecundity.

  23. Upright Biped on UD:

    I’m hoping Keith’s and Onlooker show back up with their “revamp” of the argument at the top of the page.

    I would have thought it would have made more sense for UB to put together his own definitive version of his “Semiotic Theory of Intelligent Design” rather than this cycle of UB producing some screed, someone paraphrasing in an attempt at clarification and UB responding with “that’s not what I am saying”. I mean, otherwise, what has happened other than some pseudonymous commenter has mused about his incredulity on the origin of biological processes involved in protein and RNA synthesis.

    Upright Biped, if you want to be famous (and if you have really come up with a theory of ID which everyone else has missed in the fog of words you will be famous), why not distill your thoughts into a proto-paper that you could publish on your own blog (WordPress or Blogger are free) or at UD or EN&V. Gpuccio seems to be willing to help you with a better understanding on the biochemistry and I am sure Joe and Mung can brighten the prose with a few choice phrases. I think that is all UB can expect from the fair-minded observer.

    Until then, it is hard to disagree with Keith’s assessment that all you have produced so far is a classical example of an argument from personal incredulity:

    The Great Semiotic Theory of ID, which Upright says he’s been working on since 2009, is nothing more than the hackneyed ID Argument from Incredulity. Upright doesn’t see how it could have happened. Therefore the Designer did it.

  24. Forgot to add the link in onlooker’s comment that I copied and posted above

    http://www.uncommondescent.com/design-inference/it-seems-that-tsz-objector-to-design-af-insists-on-the-long-since-corrected-canard-that-design-is-a-default-inference/#comment-433602

    @ onlooker

    Your first comment went straight into spam, possibly because you included a link. You should be able to post comments already but, if you like, post a test comment in the thread ” Apologies to Kairosfocus and Petrushka” and I should be able to clear you from pending. 

    Where’s Lizzie!!! 

  25. Joe:

    Allan Miller sez:

    Three physical DNA bases are not a ‘symbolic’ representation of an amino acid. It really is that simple. In certain circumstances, a particular triplet of DNA bases may be involved in a causal molecular chain that results in a particular amino acid getting stuck on the end of a peptide chain. Equally, it may participate in regulator binding, or be edited out of mRNA, or cause nothing more than its complement to be added during DNA replication (which as a minimum all bases do, wherever they sit).

    Joe: What a dolt!

    Ah, I see KF’s civility leash is slipping. And TSZ is so not-worth-mentioning, Joe is spamming the thread with references to it! I’m sure the average UD-er is saying “Who is Allan Miller, and why am I supposed to give a shit what he thinks?”.

    The argument pertains to transcription and translation in which the codon DOES represent the amino acid.

    What is wrong with you guys that you are forced to erect strawman after strawman in an effort to distract from the fact that your position has absolutely no evidence? Oh, never mind, I answered the question with the question…

    “Strawman” appears to be a word that you and your ilk blurt out as shorthand for “I don’t really understand”. A triplet that finds itself in the translational frame suddenly comes to ‘symbolise‘ an amino acid? Nah – the two are simply elements in a causal chain of physical interaction.

    Acid-bound tRNAs are like paintbrushes each dipped in one of 20 colours, with up to 61 different handles. It is, IMO, stretching a point to suggest that the holes into which the handles fit are a symbol for the colour at the end of the brush. They can be read as such by investigators, but that’s not what the physical system does.

    But ultimately … whatever. You can call a codon a symbol if you like; I’m not sure why you think it such a big deal to define it so. Because all that really matters is whether the linkage between codons and amino acids can evolve. And of course it can, precisely because ‘paint’ and ‘handle’ are independent, coupled through tRNA – and you don’t even need the bulk of that molecule, or mRNA, to achieve ribosomal peptide synthesis.

  26. Joe asks

    If ID is an argument from personal incredulity, what does that make YOUR position, Alan- seeing it doesn’t have any evidentiary support?

    One strong conviction I currently hold is that UB has not presented an “argument for intelligent design”. My conviction would be easily falsified with contrary evidence in the form of a coherent argument or hypothesis. Ideally, it should be a better explanation than any previous hypothesis. 

    I say it makes it an “argument” from your arse. Do you agree?

    I’m not making an argument, Joe. Like everyone else who has tried to fathom the depths of UB’s “semiotic theory”, I am just suggesting he make some effort at clarification. At the moment, consensus is UB’s argument is nothing more than the usual default of “I find current scientific explanation for X unbelievable, therefore design”.

    link
     

  27. link

    UB:

    You are spot on!

    This Lenski affair is clearly a (very interesting!) tweaking of regulation of existing funtions, in the presence of extreme environmental stimuli. Moreover, it is probably adaptational in nature (something bacteria are very good at), and therefore probably helped by existing algorithmic information (in line with what has been recently outlined in the thread about “guided evolution”.

    But, obviously, our friends in the other field will acclaim the evolution in action and the dFSCI generation by unguided mechanisms!!!!

    But, gpuccio, do you not see that Lenski was only manipulating the environment? The environment in this case, as in life in general, is the designer. Lenski provided the empty niche. Eventually a lucky mutant ended up and flourished in that niche. Selection is not random.

  28. Me: A triplet that finds itself in the translational frame suddenly comes to ‘symbolise‘ an amino acid?

    Joe: The codon is a REPRESENTATION of the amino acid. There isn’t any physio-chemical connection with the codon and the amino acid it represents- meaning there isn’t any physio-chemical connection that determines which codon represents which amino acid- ie it is arbitrary, yet it is maintained throughout living organisms.

    Whoosh! Representation, symbol …? Aren’t they synonyms? I explain why I don’t think it reasonable to say that the codon is a symbol/representation of the amino acid … and Joe sez: it IS! it IS! it IS! Fair enough Joe, you think it is, I do not. And as I went on to say: it does not matter a damn. It does not become less evolvable simply by insisting it is ‘symbolic’, and indeed the ‘arbitrary’ independence of parts is precisely what allows the possibility of change – in organisms in which it is not deeply embedded. Which of course excludes every modern organism, since it was already embedded in their ancestors. 

    there is no physio-chemical connection with the codon and the amino acid

    And again this mangling of terms. Physico-chemical goes on the pile along with moles, epigenetics, natural selection, random, nested hierarchy  and a few dozen other terms with that uniquely Joe spin:  …. what the hell are mRNA, tRNA  and aaRS, do you think? They form a physico-chemical chain!

    physicochemical[ˌfɪzɪkəʊˈkɛmɪkəl]

    adj
    (Chemistry) of, concerned with, or relating to physical chemistry or both physics and chemistry

    Translation involves an entirely physico-chemical chain of binding, bonding and diffusion. To say “there is no physio-chemical connection” is like saying there is no connection between the fire and the well because water is transferred through a bucket chain.

    Me: Because all that really matters is whether the linkage between codons and amino acids can evolve.

    Joe: Evolve how? How can we test if it evolved via blind and undirected chemical processes? Can you provide a testable hypothsis for such a thing?

    Evolve by independent amendment of binding sites, in tRNA, aaRS, ribosome etc. You think we need to actually do that, in a given system, before we can determine whether it is plausibly possible in that system? Such modifications are rather fundamental to evolution in general, so if you have something to offer that the chemists and geneticists have overlooked, you’d best get onto them right away. I’m sure they’ll be fascinated to hear from you.

     

  29. Alan Fox: “But, gpuccio, do you not see that Lenski was only manipulating the environment? The environment in this case, as in life in general, is the designer. “

    This is something ID will never be able to admit to.

    They find it hard to believe given the alternative, the “Theory Of Magic”!

  30. Joe: “A non-material designer has all the matter in this material universe at its disposal- especially if it designed this material universe. “

    A “non-material” designer cannot even “touch” matter since he has no matter to “touch” with.

    BA77 would probably give you a good argument that it’s like a disembodied “near-death experience” where the “patient” can’t get anyone to hear him, because his “non-material” vocal cords cannot interact with “material” air.

    What you are suggesting Joe, is that the “laws of physics” in no way restrict the designer.

    If this is the case, there is no reason for chemistry in the cell at all.

    The brain could simply control all body activity directly with “symbols” sent through the nervous system.

     

  31. Joe: “A non-material designer can manipulate matter using energy- just as I said. “

    Onlookers would like to know why you don’t have an answer to *how*?

    1) ID doesn’t need to answer *how* questions because God already knows *how*.

    2) ID doesn’t need to answer *how* questions because that’s in the realm of science.

    Which is it Joe?

     

  32. Joe,

    Why have any cell chemistry at all if “material” processes can be controlled by “non-material” thoughts?

    If the “designer” uses “non-material” control over biology, why didn’t he give us that capability?

     

  33. Is the designer’s energy subject to conservation laws? If matter is being moved, energy is being transferred to it. If that energy came from outside this material universe, without any balancing transaction, it would be a violation of this universe’s Law of Energy Conservation. Which is obviously not set in stone, but it is fairly robust!

    Energy is also a form of matter – or, matter is a form of energy. E=mc2 and all that.

  34. That’s a good thought!

    If “m=0” for a “non-material” designer, then “E = 0”!

    Wow!

    A “non-material designer” would have no energy besides having no matter!

    Joe, what’s up with that?

    kairosfocus, anyone?

     

  35. Allan,

    Is the designer’s energy subject to conservation laws? If matter is being moved, energy is being transferred to it. If that energy came from outside this material universe, without any balancing transaction, it would be a violation of this universe’s Law of Energy Conservation. Which is obviously not set in stone, but it is fairly robust.

    The Designer can do anything you want Him to. It makes Him an ideal gap-filler.

  36. Upright BiPed, UD’s “rose coloured glasses” poster boy, again re-writes history! 🙂

    1) UB: 2 + 3 = 6.

    2) RB: That’s an invalid use of “+”.

    3) UB: Does 5 + 5 = 10?

    4) RB: Yes, that is a valid use of “+”.

    5) UB: AHA! You’ve finally conceded 1) is valid!

    Joe, do you buy this?

     

  37. Upright BiPed: “I was there to debate Bill. We debated. He lost. “

    The debate was actually about what your “semiotic theory of ID” was about.

    By the middle of the “debate”, *neither* side knew what your point was.

    In that sense, the “debate” about “what you were talking about”, was actually a draw!

     

  38. I haven’t had a chance to look. but If gpuccio has responded I bet he hasn’t responded to the really interesting finding in the Lenski experiment.

    That would be the neutral drift in the first 20,000 generations that had no discernible effect on the use of citrate, but which were nevertheless necessary precursors.

    How does the designer intelligently select neutral mutations? How does it know which mutations will be needed in the future?

    Here is an experiment that documents in real time all the evolutionary mechanisms that have been inferred from comparative genomics. It’s the Halley’s comet of TOE.

    But I’m still wondering if the series of mutations could have been sped up by intelligent selection. If design can’t demonstrate it’s advantage in this incredibly simple scenario, how can it possibly claim to have an advantage in more complex scenarios? 

    Perhaps GP has already answered all this, but I’m at work and can’t look at the moment.

  39. Gpuccio at UD

    writes:

    What we observe in Lenski’s experiment is true RV + NS OR true adaptation. I don’t think we can really distinguish, at present. Anyway, it is not design. And indeed, the result has not the characteristic of new design.

    You may be interested in Richard Lenski’s own view in an email to me on whether his experiment was indeed natural selection, I quote below

    Hello Alan,

    Thank you for the kind words. I would describe selection in the context of my long-term E. coli experiment as “natural selection in an artificial environment” for the following reasons:

    It is an artificial environment that was constructed to be simple, reproducible, and tractable. It allow us to address basic questions about the process of evolution, rather than to understand how this particular species makes its living in nature.

    It is natural selection because we do not choose which individual cells survive and reproduce based on their properties. Rather, the interaction between the organisms’ phenotypes and their environment causes some genotypes to be more successful, on average, than others. (“Genetic drift” – that is, the effects of random sampling of cells during the serial transfers – also influences the fates of genotypes. Selection, though, acts through the systematic tendencies of different genotypes and their resulting phenotypes toward greater or lesser success.)

    Best wishes, Richard Lenski

    On 2/18/11 11:53 AM, Alan Fox wrote:

    Dear Professor Lenski

    Having become aware of your tremendous contribution to evolutionary biology on reading Dawkins “Greatest Show on Earth”, I thought it a great example of demonstrating evolution in action and proposed it as such in a discussion at Biologos.org (a website set up by Francis Collins to wean Evangelicals away from Creationism – or, at least, I think that’s its purpose). There was then some disagreement whether your long-running experiment demonstrates “natural selection” or ought more fairly be described as “artificial selection”. Would you be able to comment as to whether either description is apt?

    The actual thread is at

    http://biologos.org/blog/celebrate-science-dont-fear-it/

    I don’t know if you recall the Woody Allen movie where someone in a queue is arguing interminably the views of Marshall McLuhan, when Allen produces the man himself to silence the arguer. Any response you find time for, either as a response to this email or directly, would be greatly appreciated . Thanks in advance and thanks for your contribution to scientific knowledge.

     Sincerely
    Alan Fox

  40. Anyway, it is not design. And indeed, the result has not the characteristic of new design.

    So we can add gpuccio to the list of ID advocates who simply define themselves as the winner of any debate. here we have a slow ball over the plate that ought to be a home run for a designer, and Casey says “That’s not my style.”

  41. Joe: “Onlookers would need to tell me how that is even relevant- we don’t have to know how designers did it BEFORE we can determine they did. Obvioulsy evos have no clue how science operates. “

    In police investigations, they look for motive and opportunity.

    ID’s “designer” may have had “motive” but if he *couldn’t* actually do it, he had no “opportunity”!

    Allan Miller: “Energy is also a form of matter – or, matter is a form of energy. E=mc2 and all that.”

    If your designer was “immaterial”, he had no “mass” and therefore, no “energy”.

    If ID is not constrained by the “laws of physics” then ID has to admit, this is NOT a scientific argument at all.

     

  42. Joe: “Ever hear of telekinesis, ie thought energy? “

    Are you saying that ID claims “telekinesis” as one of the mechanisms that brought about the OOL?

     

  43. Upright BiPed,

    Joe: “Ever hear of telekinesis, ie thought energy? “

    UB, is “telekinesis” the mechanism used for the “transfer of information” into the first living cell?

     

  44. UB:

    Upright BiPed: “I was there to debate Bill. We debated. He lost. “

    He forgot, “Then I left ’em hanging. I cut and ran. Absconded. Beat a retreat. I blew that pop stand. Bolted. Decamped. I slipped out the back, Jack. Flew the coop. Got the hell out. I made off. I exited, stage left. I scampered. 

    All of which ‘successfully confirm’ a glorious victory for ID.”  

  45. Mung: “And God said, “Let there be light,” and there was light. “

    So ID is based on scripture, not science.

  46. He forgot, “Then I left ‘em hanging. I cut and ran. Absconded. Beat a retreat. I blew that pop stand. Bolted. Decamped. I slipped out the back, Jack. Flew the coop. Got the hell out. I made off. I exited, stage left. I scampered. 

    All of which “successfully confirm” a glorious victory for ID.”

    You might say those are the ‘entailments’ of ‘victory’, ID-style. 

Leave a Reply