KF vs Toronto & Petrushka

Over at UD, KF has started a new thread criticizing Toronto.  He had earlier started a thread criticizing Petrushka.

It would have been nicer if KF had joined here to launch his criticism, instead of taking pot shots from UD where it is my understanding that both Toronto and Petrushka have been banned.

In any case, this is where the two accused can set the record straight by explaining what they actually meant.  Others can join in.  I may add something later.

Let’s keep it polite.  No character attacks.  Let’s stick to clear explanations of positions that KF might have misunderstood.  And let’s remember the rules of The Skeptical Zone and keep it civil.

Open for discussion.

192 thoughts on “KF vs Toronto & Petrushka

  1. KF writes:

    Seversky: Weasel, as simple as it is, shows one aspect of evolution, i.e. selection, at work.

    Do you have anything like that?

    Obviously, T has failed to do basic homework and does not know that Dawkins has admitted that Weasel is a pre-loaded targetted search. Cf here.

    Weasel just shows that selection works it is a child’s toy compared to what can be and has been done with genetic algorithms. If you want an example of a toy algorithm that uses Markov selection and is a notch more interesting than Weasel, try this:

    http://itatsi.com  click the Start button.

    It has no goal and no target. Just a sparse functional landscape in which the drunk can walk in any direction and arrive at any destination. It does not claim to be a model of evolution, but it is a demonstration that functionality (in this case, long words) can be reached by a drunkard’s walk.

    There are around four billion possible ten letter strings and just a few thousand ten letter words, and yet these words can be reached by the drunk. Even more interesting to me, the drunk can reach ten letter strings that are not in the dictionary, but look like words, are pronounceable, and sometimes meaningful. In other words, the program invents new words.

    But even this is just a toy. It was written to demonstrate that a sparse functional space can be explored without having a target.

  2. if sequence space is as sparse as KF claims it to be

    I’m too pressed for time to dig it out, but I found a fascinating paper that generated 1.5 million ‘random’ completely synthetic 105-residue peptides based upon a simple rule that ensured that they folded. Several sequences from this library rescued E Coli knockouts, despite having no sequential or structural relation to the deleted protein. This shows a remarkable degree of functional richness in the region of protein space that enzymes actually occupy. It isn’t ‘new’ function, but does give a rough guide to the extent to which proteins other than the ones we actually have at a particular locus would have done the job. I’ll try and find it when I’ve been for a run.

  3. kairosfocus: “All that is required is that a designer is POSSIBLE, not impossible. “

    Then SHOW that a designer is possible.

    Let’s say I’m the designer and I  want to design a life form that will work 100 years from now at the north pole.

    How do I know whether there will still be ice there?

    What kind of food would be available in a hundred years?

    How do I know if a >500 bit change in the DNA will result in the change I want for an environment that I can’t determine?

    If your designer doesn’t have the answers to these questions, the existence of your designer is more unlikely than evolution.



  4. kairosfocus: “You know or should know that I have publicly rebuked Joe for his behaviour, explaining why it is wrong and should be corrected. Joe is on probation and is subject to further action at UD. I do not control moderation at UD, as I have stated. 


    THAT, FYI is the sort of reason why I will not come into your lair at TSZ or elsewhere. “

    It is your decision to NOT come here because of the way we behave, but you have also decided that you WILL contribute to a site that houses the incivility of Joe.

    It’s not Joe that’s the problem, it’s you.

    You can’t claim we’re too uncivil for you anymore as you accept Joe’s civility to be good enough for you at UD.



  5. Joe: “Take away the personal attacks on myself and other IDists and Creationists, take away the equivocations, lies and misrepresenations, and I can be as civil as anyone can be. “

    If you cheat on your wife, does she have a right to a free affair?

    Bad behaviour on the part of subject A does not justify the same behaviour from subject B.

    Ask WJM about morality.


  6. Joe: “Who wants to post on a forum in which he just gets personally attacked? “

    Then tell Barry to clean up his act and start treating fellow debaters with respect.


  7. I understand the desire to correct the nonsense being spewed on UD (SIWOTI!), but this dual-blog exchange just gives the IDCists the attention they want without the need to venture from behind the safety of Barry’s skirts in their echo chamber.

    Of course I can’t control anyone else’s behavior, nor would I want to, but I’m choosing to respond only to those with the minimal intellectual courage required to post here.

  8. That makes for a lot of empty weeks.

    In my view there is an obsession with winning at the expense of communication. I’ve seen this from both sides.

    Of course I think the other side is the guiltier. why else would they ban and censor people who don’t violate they written rules?

    And speaking of written rules, what sense does it make to have a rule that your core positions are out of bounds? What sense does it make to assert the very claims that are being questioned are already answered?

    But I have enjoyed a few moments when the opposition engaged in conversation rather than holy war. Such moments are rare.


  9. Toronto,

    Good point, and I had every intention of doing that before I started! 

    It’s a daily struggle.  I was clean for Lent, but fell off the wagon a couple of weeks ago.  I’m better now.

  10. petrushka,

    That makes for a lot of empty weeks.

    In my view there is an obsession with winning at the expense of communication. I’ve seen this from both sides.

    While this probably violates Lizzie’s site rules, I don’t believe the denizens of UD specifically or the intelligent design creationists more generally are interested in bidirectional communication.

    The fact is that there is no scientific theory, or even hypothesis, of intelligent design.  It explains no observations and makes no predictions.  There is no reasonable doubt after this many years that ID is anything other than a fundamentalist Christian political movement.

    The only reason to pay any attention to the IDCists is because of the political power their base wields.  It is important to prevent them from destroying science education.  If they didn’t pose that threat, they’d be of no more intellectual interest than the flat earthers or Velikovskyites.

    So you’re damn right — our focus has to be on winning.

    But I have enjoyed a few moments when the opposition engaged in conversation rather than holy war. Such moments are rare.

    I enjoy a good debate more than most. It would, however, be foolish to ignore the history and clear goals of our interlocutors. These people want their religion in our schools. They must be stopped.

  11. I would like to post an open challenge to KF. Since he wants a thread “for the record,” I would like to go one on one with KF. I would prefer that other posters abstain, but that is not a requirement.

    All I ask is that this take place where I can post. I’m willing to do it at UD, even if I am only allowed to post on one thread for a limited time. My only demand is that I will not be censored unless I engage in name-calling or some equivalent infraction. By limited time I mean at least a week.

    The topic I suggest is whether ID or evolution is the best explanation for the diversity of life. If the discussion takes place, I will elaborate on this.

    So it’s in your court KF. Are you willing to take on one lone evolutionist for a time limited discussion?

  12. Thanks Joe, for posting a link to my challenge. I will allow KF to determine how he wants to present his case. The only limits I request is that the discussion be limited to biological facts and theories and not wander into politics. I don’t mind if KF brings up politics, philosophy and theology, but I don’t intend to respond, because I have no knowledge in these areas.

    My desire is to have a conversation, a give and take, rather than a debate. But again, I’m not fussy about how other people characterize it.

  13. I’m willing to do it at UD

    Not that I expect kairosfocus to take up your challenge, but if he does I hope that you will post a copy of your comments here or in some other venue not subject to UD control.

  14. I appreciate that there is a political aspect to this, but that is beyond my power to control. My interest is to sharpen my own understanding. I have no personal gut fear of being wrong. I’m not even particularly fearful of having my ignorance — of which there is quite a bit — exposed.

    I just enjoy the discussion. I’m not dancing in the streets in pre-celebration. I’m just expressing my interested in having a clean give and take discussion.

  15. I appreciate your calling attention to this, Joe, but I think KF can evaluate the prospects for himself. He is free to define ID any way he pleases, and he is free to correct any definition I might present.

    It will presumably be his thread, so he will have the ability to counter anything I say using any argument he chooses.I merely stipulate that I have no training or experience in philosophy or theology. So I may not have any response in those areas.

  16. Petrushka,

    I mentioned in a reply upthread that I had a paper illustrating a function-richness in a small area of ‘protein sequence space’ that helps shed some empirical light on the question, preferable to the heat of competing assertions. I had thought about submitting it as a ‘journal club’ post.


    The authors constructed a library of 1.5 million 102-acid peptides, designed to fold in 4-helix bundles but with no design of function. 27 ‘natural’ genes of considerably greater length and structural complexity in E. Coli were deleted, and the library assayed on the basis of ability to get these mutants growing again.

    And of their library of 1.5 million, they found 18 artifical sequences, with no designed homology to the deleted proteins, that were nonetheless able to rescue function in four of the 27 knockouts. Bearing in mind that the search was restricted to functional analogues of just 27 proteins, this is quite an impressive hit rate.

    There are 4000 other genes in E. coli. It is highly unlikely that they just struck lucky with the genes they chose. More likely is that this library, a tiny subset of the 20^102 20-acid possibilities, itself a subset of larger proteins, is rich with function, if we could assay the whole of the protein set with the ease we can plate out E. Coli nutritional mutants. And if we could extend the assay to the 10′s of thousands of proteins in millions of other species …

    This paper also demonstrates the extensive chemical redundancy of the genetic code – their method of building the helixes exploited this feature. Calculations of the type I just did – 20^102 – are extremely misleading in the huge numbers they yield, and the frequent assertions that 20 acids are some kind of magic number for function are simply biochemically naive.

    Design fans will point out that these peptides are not truly ‘random’ – but then, neither are evolved ones. Apart from the dawn of protein synthesis, evolution starts from something that already works: a folded functional catalyst. So excluding random peptides that do not fold is entirely legit. There is, by the same token, no reason to suppose that proteins that fold in this particular way are anything special. Either way, for obvious reasons, you have to do some restriction. There is not enough carbon in the world to make every possibility.

    They will also point out that this is not new function – but it nonetheless demonstrates that ‘landing’ on a different function is much more likely, given a function-rich space, than is hoped for in the ID world.

    Also worth noting that this work was not aimed at assaying sequence space for function richness, per se, but simply trying to find functional synthetic peptides.  

    There’s a lot more I’d like to say, but it’s hard to get it all in a blog comment. I can hear the ID enthusiast yelling “red herring nice strawman!” as I type, which is rather distracting!

  17. I’ve seen that. I can’t memorize the details, but they lurk in the back of. My mind. My goal in a discussion is not to win, but to explain clearly why I believe what I do. My fantasy is not to convince anyone, but to arrive at a point where each side can paraphrase the other’s position.

  18. I’m embarassed.   Apparently part of KF’s massive reply was aimed at me, and I just didn’t notice it!   At one point, after describing other people’s arguments and rejecting them, he says:

    KF: JF then goes on to suggest that the origin of two sites worth of information and a hypothetical example are adequate to overturn the observations on the source of FSCO/I and the analysis that shows why 500 bits of de novo information is a reasonable threshold for de novo info from an arbitrary start point being reasonably attributed to intelligence.

    Of course, beginning in an existing island of function and moving around a few bits at a time through some form of hill climbing is not relevant to the matter, as it begs the question at stake: how to get to the shores of an island of function across a deep isolational barrier from an arbitrary initial condition. And that basic challenge does not begin from already existing life — a big begged question — but from some warm little pond or the like pre-biotic environment.

    He is referring to my comment in this thread on 25 August above, where I am pointing out that William Dembski’s Law of Conservation of Complex Specified Information is both unproven, and in the form in which it is stated, unable to show that one cannot accumulate 500 bits of Complex Specified Information (even if the theorem were proven).  In my earlier post (linked in the preceding comment) I showed a simple numerical example of the accumulation of 100 bits of CSI.

    KF misunderstands Dembski’s argument.  It is not about islands of function, and it is intended to apply to evolution after the Origin Of Life.

    KF: This issue is often begged in the context where there is no empirically supported causally adequate chance and necessity mechanism to get us from chemicals in a pond or the like to a functioning, encapsulated and gated, metabolising digital coded information using self replicating form. But, observed cell based life is full of things that in any other context would be immediately recognised as strong and reliable signs of design: digital code, algorithms, organised information processing and cybernetic machinery etc etc etc.

    Sorry, Dembski is not talking only about prebiotic evolution, he means his argument to apply to evolution after the OOL.   I can only suppose that KF feels Dembski’s argument does not apply for evolution after the OOL.  (Would that mean that KF thinks that more than 500 bits of CSI could get into the genome after the OOL?)  I have read Dembski very carefully and it is quite clear that he does not restrict his theorem to the OOL.

  19. Fisher et al., De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth, PLoS One 2011. 

  20. I posted this further up the thread:

    A comment on Kairosfocus’s abduction to arrive at a best explanation for the OOL.

    A is known to be a source of B

    No other source of B is known.

    Therefore, I infer that A is the best available explanation of any B.

    That kind of abduction seems to work well when A and B are specific well described things. Humans and written language, for example. If archaeologists discovered an ancient tablet with symbols that appeared to be writing, they could reasonably infer that humans were responsible. It’s not a proof. Aliens could conceivably have visited the planet and done some scribblings, for example, but humans are currently by far the best explanation.

    The above type of abduction is what Kairosfocus seems to believe he’s doing.

    But this is what Kairosfocus really does.

    A is known to be a source of B

    No other source of B is known

    Therefore, I infer that an unknown C which shares a property with A is the best explanation of any D which is similar or analogous to B, and could be given the same broad description.

    And he ends up with non-living intelligent designers, something not known to exist, as a best explanation for the origin of life.


    Kairosfocus replies on U.D. The bits in brackets [like this] are my comments on his reply.

    Looks like Dr Who is trying for at least a bronze in the poster-child category: “this is what Kairosfocus really does.

    A is known to be a source of B

    No other source of B is known

    Therefore, I infer that an unknown C which shares a property with A is the best explanation of any D which is similar or analogous to B, and could be given the same broad description.

    And he ends up with non-living intelligent designers, something not known to exist, as a best explanation for the origin of life.”

    He apparently does not realise that the challenge he imagines is unique to design theory is faced by all forms of scientific investigation. As the OP above shows, the way we look at the issue in science is we examine causal factors that reliably produce as reliable signs, the traces we have from the unobserved past. On that we may make an inductive inference to best current, and provisional explanation. As, with all of science on the past of origins.

    But to avoid acknowledging that, DW plays a strawman tactic:

    [Strange. There's nothing in my post to indicate any of this. Quite the opposite. I give an example of a reasonable abduction in archaeology. But let's go on to my supposed strawman.]

    I infer that an unknown C which shares a property with A is the best explanation of any D which is similar or analogous to B

    KF: Simply wrong.

    FSCO/I is a very familiar entity and it is well known that it comes from design, and on the needle in the haystack analysis, it is not plausible that it should result from the other source of high contingency, chance, on its own or in concert with mechanical necessity [which is NOT a source of high contingency].

    All that is required is that a designer is POSSIBLE, not impossible.

    [Well, my point has been missed. To make inductions and abductions, make sure the "As" and "Bs" remain the same things, and keep them as specific and well defined as possible. If you observe that some "FSCO/I" is produced by humans (A), then infer that all of it is. Also, make sure your "familiar entity" isn't too general. Remember, humans can intelligently design fire, hills, nuclear power sources, waterways and many other things that can be found in nature. Get more specific, and you've got campfires, burial mounds, nuclear power stations, and canals. You can see how you're less likely to make mistakes with your abduction the less general your "entity" is.

    Do you now understand what I mean by adding Cs and Ds to the As and Bs we should be sticking to?]

    KF:, one seemingly driven by DW’s own a priori commitment to materialism as a worldview:

    “he ends up with non-living intelligent designers, something not known to exist, as a best explanation for the origin of life.”

    [It does not require any kind of worldview to make the observation that no non-living intelligent designers have ever been discovered] 



  21. kairosfocus:”Only when there is a clear understanding of why the two sides take different positions across the range will we be able to resolve the matter properly. “

    I think all we should care about is what we teach students.

    Our side has a mechanism to offer, yours doesn’t.

    We can say, “This is how our theory works”, and you actually refuse to even make an effort to come up with one.

    Until you have a mechanism of your own that can replace ours, we are under no obligation to take you seriously.


  22. Hi, Kairosfocus.

    Let’s do abductive reasoning.

    Life is a chemical phenomenon.

    Unintelligent chemical processes are known to create chemical phenomena.

    Humans can intelligently design chemical phenomena.

    Humans were not present on the early earth when life first appeared.

    No other intelligent beings are known to be able to intelligently design chemical phenomena, or to have been present on the early earth.

    Therefore, I infer that unintelligent chemical processes are the best explanation for the origin of life.

    I hypothesise that chemical reactions and chemical evolution led to the first life form(s).

    Kairosfocus hypothesises that non-living intelligent designers created the first life forms.

    Chemical reactions and chemical evolution are both directly observed realities.

    Non-living intelligent designers have never been observed to scientific knowledge, and are not even known to be possible.

    Therefore, there is virtually infinitely more evidence for my hypothesis than K’s. Therefore, it is clearly the best current general explanation for the OOL.

    Here’s another example.

    Humans write books.

    There is no other known source of books.

    Therefore, human authorship is the best explanation for any book of unknown authorship, and it is reasonable to infer that all books were authored by humans.

    Do you agree that that’s good abductive reasoning, Kairosfocus?

    I ask, because it might not be popular at Uncomon Descent if applied to a certain famous ancient book.

    In fact, some of your colleagues might not be too fond of abductive reasoning in general.

  23. Joe: “Our mechanism is “design by an agency”. “

    If our mechanism was as non-existent as yours we would call it, “design by birth”.


  24. Someone not banned at UD should give Dembski an invitation to present his case here.


  25. Thanks to keiths for pointing out this.

    Dembski: “Yes, these bacteria are gaining new information, but they are gaining it from their environments, environments that, presumably, need not be subject to intelligent guidance. “

    There it is, a gain of CSI without intelligence!

    kairosfocus and Joe, are you going to correct Dembski?


  26. kairosfocus: “You further know or should know that the critical issue with EL was, and is, enabling behaviour for the uncivil; “ 

    UD enables Joe.

    Are you going to keep posting there regardless?


  27. Joe: “We know there isn’t anything we can say to convince you of the merits of ID. “

    If CSI is information that necessarily is the result of an intelligence, you would have a much easier time of simulating it than we would an evolutionary model.

    Show in your model how you would analyze a future environment before you actually start designing the >500 bit biological change required.

    Note that I’m not even asking how to make the biological design change. I’m simply asking how would you identify the “specification” required in the future.


  28. Joe kindly attempts to reason with me on U.D.:

    Joe: “Earth to dr who:

    dr who: Kairosfocus asks whether or not abductive reasoning can be valid in science in his first point. I’ve agreed that it can be, and shown him how it’s done to effect, and what the results would be in relation to the OOL. I know what I’m doing, and why. I’ll explain in detail sometime.

    What is the evidence that life is ONLY a chemical phenomenon? Oh, that’s right there isn’t any such evidence so your “reasoning” fails at the start.

    Also Christians are OK with humans authoring the Bible.

    But please keep ignoring that and pressing on anyway. You make my point for me-> that it is a waste of time trying to reason with you.” /Joe

    I’ll take that to mean that Joe suspects that my reasoning to the best explanation would be correct on condition that there’s nothing other than chemicals in the basic physical composition of life. Otherwise, he’d have thought of a better objection.

    The evidence, Joe, is that’s all we observe when we actually physically examine life. Being a chemical phenomenon doesn’t mean that it can’t have emergent properties, which it certainly does have.

    As for the Christians, I’m glad to hear it, and delighted that they’ve all appointed Joe as their spokesperson.

    As for time wasting, Joe’s participation is entirely voluntary, and my post wasn’t addressed to him, but I always welcome his contribution as I personally regard him as one of I.D.’s finest thinkers. 

  29. Joe still seems to want to try and make the case that life isn’t a chemical phenomenon on two more U.D. posts. I wonder whether he’ll realise that he’s undermining something that Kairosfocus claimed earlier on the same thread.

  30. The consistently foolish are the hobgoblins of little minds.

    It strikes me that he is undermining Upright BiPed also. If there’s anything admirable about UBP’s theory, it is its lack of ghosts in the machine. UBP seems to believe that ghosts created the machines, but he has ruled out spooks in the operation.

  31. kairosfocus: “Criterion of Adequacy (CoA):

    As evidence accumulates, the degree to which the collection of true evidence statements comes to support a hypothesis, as measured by the logic, should tend to indicate that false hypotheses are probably false and that true hypotheses are probably true.”

    The existence of a designer is itself an inductive argument.

    The designer’s abilities are also an inductive argument.

    How did you determine the designer exists?

    How did you determine his abilities?

    How much truth is there in these premises?


  32. So true.  Either the ghost is in the machine, or the ghost created the machine.  It can’t be both.  Or at least you can’t argue rationally that it’s both. 

    This is one of the easiest ways to see that ID proponents are simply praising the lord, and nothing more.  You can’t argue on the one hand that an object is designed because it’s so complex, and then also argue that the object needs miraculous intervention to work.  But that’s exactly what ID proponents argue at every level from the atom to the entire universe.   




  33. Is it me, or has the whole ID “movement” degenerated into a series of individuals talking past each other?
    There seems to be some serious mutual undermining going on, with not one of ‘em bothering to try and understand the import of what any of the others are trying to say. 

  34. kairosfocus: “What I laid out is the Darwin’s pond challenge that Evo mat advocates have by implication set for themselves, and the big gap they face is where do functionally specific complex organisation and associated information come from once their favourite out, natural selection, is off the table at OOL “

    A good design question that asks, where does the designer get the information for the functionality required in a future environment that does not yet exist?



  35. kairosfocus: “The key way out of it is the multiplication of lines of investigation that are sufficiently distinct that massive coincidence is ever more unlikely. “

    So if design is likely, but a designer with the necessary abilities is not, where does that leave the possibility of ID?


  36. I simply cannot penetrate KFs latest ‘questions’ post. We take a long time to get to any questions – half a post in and we’re still smarting over the very notion that one could say ‘don’t link to porn’ in a lighthearted manner (ask Joe – he appears to have a sense of humour), and lots of old-favourite expressions about distractions and attacks. All of this bluster from KF seems designed to distract from a fundamental lack of substance.

    I haven’t seen any attempt to address the apparently significant density of functional packing of protein space on an evolutionary scenario, as per the several papers linked above and elsewhere. Instead, the goalposts have moved yet again, back to the OoL – a process about which we know next to nothing. And KF demands to know how we got ‘information’ out of this unknown process. Since we know nothing about it, we really cannot say whether it was within or outside some arbitrarily-assigned ‘probability bound’. Nor can they say how any designer got round the various problems, come to that (including his existence), rendering this a pointless set of questions – “how do YOU explain something whose parameters and constraints are unknown?”. Dunno.

    Now KF and Joe insist that nucleotide translation is NOT a chemical process.

    Joe: For the record, the translation of nucleotides into amino acids is not a chemical reaction and cannot be described by chemical reactions.

    KF: Not only so, but the CCA- coupler is a universal joint in the tRNA. It is the “loading enzyme” — note the Chicken-egg loop — that determines which AA goes with which tRNA. In short, this is an INFORMATIONAL correspondence, not a chemical one.

    Anyone with a basic grounding in biochemistry would be able to point out how utterly wrong this is. Is it because there is hydrogen bonding involved? Is that not felt to be ‘chemistry’, but instead some form of ‘informatic’ exchange? Is the hydrogen bonding in protein folding ‘informatic’ too, or that which keeps your hair from falling out, or water liquid to 100 degrees?

    The distinctive bases distal to the tRNA ACC stem form a particular shape, with vital hairpin motifs and certain essential base pairs, all with a 3D shape. They are bound by hydrogen bonds, not ‘informatic bonds’, in the ‘loading enzyme’. Only the right shape will bind, but this is a property common to all enzymes – chemical catalysts one and all, with substrate recognition by shape, charge density and hydrogen bonding. There is nothing different about the ACC stem in this regard, while the supposedly ‘informatic’ anticodon does not come into tRNA recognition.

    ATP is then covalently bonded to the amino acid, which is then esterified to the Acceptor. This is chemistry. The tRNA anticodon hydrogen bonds to mRNA, which physically holds it in place by shape alignment enabling the energy of the amino-tRNA link to be transferred to drive peptide bond formation. Again, all chemistry. But not certain, nor even likely, to be involved in the OoL (about which, you will recall, we know nothing).  

    No doubt another million words are simmering on the matter of good faith, straw men and oil-soaked red herrings, with noises off – but I would prefer to see some basic knowledge of the chemistry of this process demonstrated by people who attempt to ‘correct’ the field on their understanding.

  37. I’m eagerly awaiting UBP’s take on this, since he has 6000 posts invested in the necessarily physical implementation of information. I expect him to show up any minute. Not.

  38. I hadn’t noticed, either, that I got a couple of passing mentions in KF’s most recent jeremiad.  First, there’s this:

    Philip Johnson’s reply to Richard Lewontin on a priori materialism in science is a classic case in point – one that is often dismissed but (kindly note, Seversky et al) has never been cogently answered:

    I’m assuming this is Johnson:

    For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.”


    Personally, I prefer the term naturalism as science, in very simple terms, is the process of trying to understand the nature of things, nature being what makes something itself and not something else.

    Materialism is the view that the universe is composed of matter and energy in all their forms and nothing else.  It is the most rational position because, regardless of what Johnson and his sympathizers might hope and believe, no one has yet shown there is anything else.  For sure, there are many big unanswered questions such as why is there anything at all, where did it all come from and what about all the counter-intuitive weirdness at the quantum level, so there is still the possibility there is something else.  But that just means there are gaps, it doesn’t mean they’re plugged with whatever your preferred gap-filler might be.

    So, for want of anything better, I can live with materialism.

    Down-thread there is this:

    Oh well, let’s see if Toronto has done the simple thing of checking what Seversky’s much despised longstanding presentations address.


    I must say I’m curious to know what these ” much despised longstanding presentations” are.

    The comment goes on to talk about Dawkins’s WEASEL illustration, which has been dealt with at tedious length elsewhere, and the presence of design.

    KF and other IDeologues give the impression that “evo-mats” are somehow denying the existence of design in the universe.  Well, we don’t.  We know full well there is.  It’s us.  We do it.  What IDeologues have yet to do is show there is anyone or anything else doing it.

    Speaking for myself, I’m quite comfortable with the possibility of extra-terrestrial intelligent designers.  Maybe the universe is teeming with ETs designing things willy-nilly all over the place.   Maybe, they’re wasting vast sums on Einstein-Rosen Bridges to Nowhere.  (I’m willing to bet they’ll all be material, too.)  The only thing we have to worry about is if any of them start having designs on our little corner of the galaxy.  But that’s just the stuff of science-fiction.  So far.

    And if there are, so what?  It doesn’t answer fundamental questions like who, if anyone, designed the designers and why is there anything rather than nothing.

    As far as I can see, the existence of extra-terrestrial designers is only poses a problem for Christians since the existence of ETs could knock us off our perch as God’s special creation, His chosen people.



  39. Joe at UD:

    I see that Allan Miller has gone off of the edge- earth to Allan- there isn’t any physio-chemical connection between the nucleotide (codon) and the amino acid it represents- the codon does not become the amino acid via some chemical reaction.

    Yes there are chemical connections/ bonds between the nucleotides. Yes there are chemical connections/ bonds between the tRNA and its amino acid. Yes there are chemical connections/ bonds between the amino acids in the polypeptide. And all of that is irrelevant to what I said.

    Earth to Joe – how does “the translation of nucleotides into amino acids is not a chemical reaction” stop being ludicrous simply because there is not a direct chemical transformation of triplet into amino acid? Of course there is a physico-chemical connection between them! It is called tRNA. The linkage just happens to occur via a series of intermediates operating on one part of the molecule or the other, and those separate parts do not interact directly during the process. But saying there is none is akin to saying that there is no connection between one end of a stick and the other, or between the slots into which the respective ends fit, because none becomes the other.

    The informatic element is imparted by us – we give letters to the bases and the acids, we can look up the relationships in tables, and they occur in strings that we can intone “Shannon” or “Kolmogorov” over. But as far as the interaction is concerned, it is entirely physical, with no more ‘informatic’ quality than the rest of chemistry. Products of one enzyme become substrates for another, and this system is the same. It simply happens that one substrate here is large, and different enzymes act on different parts of this large molecule.

    A series of 3 RNA bases – AUG, say – is simply a 3D arrangement of atoms, with which other arrangements of atoms interact. There is nothing about this that distinguishes it from any other biochemical arrangement. Either every molecule is ‘informational’, or none of them are. I could buy that they all are, in the same way that there is ‘information’ in a landscape that one could process by riding a bike across it. But the biochemical interactors of translation are ‘informationally’ distinct from every other? Typical map/territory confusion. We just call it translation.

  40. Kairosfocus responds to my abductive reasoning example with a post on the “For record” thread at U.D. I’m going to try to illustrate what he’s doing with abduction again, not for the purpose of stimulating lots of “righteous” indignation on his part, but in the hope that he might take some of the points on board.

    KF clearly wants to make the case that life is intelligently designed.

    Imagine I want to make the case that an unknown intelligent designer has designed something, and to do so in a way that seems to involve normal scientific abductive or inductive reasoning. I have only humans and their designs to point to as known examples of high level I.D. (other animals aren’t much use).

    So, here’s what I can do. I want to make the case firstly for rivers at a time in human history when we did not understand their formation.

    A can be observed to cause B.

    For this observation, I don’t want to restrict “A” to “human designers”, because then my “A” won’t cover the unknowns. So I go for the more general “intelligent designers”. I don’t want to restrict “B” to canals, because they’re not rivers, so I go for the more general waterways.

    And it appears to work, assuming a GAP in human knowledge on how rivers form.

    A is an observed cause of B

    We know of no other cause of B.

    Therefore, we can infer that the river Nile was intelligently designed.

    To support that, I could point out how incredibly improbable it is that nature would have hit the target of a river with the exact specifications of the Nile (exact length, width in all places, depth in all places), and add a Texas Sharpshooter fallacy to support my basic induction.

    KF points out, and I agree, that humans might well actually design our own life forms in the future from scratch. However, this doesn’t solve the problem, because we know that we still can’t justifiably broaden “A” from humans to “intelligent designers”. We make actual lakes, and one made by us damming a stream is essentially the same as one made by a landslide doing the same. But the inductive inference to design of lakes does not follow.

    So why does this process seem so promising to the likes of KF for the OOL? Simply because it’s a gap in our knowledge, combined with the fact that being designed is obviously personally and emotionally important to them.

    So, we’ve got the designer of the gaps. And this shows when “evo-mats” are asked for the details on how life came about naturally, whereas I.D., of course, does not have to deal with such a “pathetic level” of detail, as William Dembski would have it. It is not a mechanistic theory.

    I personally see no theory at all, and no established mechanism because living intelligence cannot be responsible for the first life.

    Dead intelligence? Extraordinary claims require extraordinary evidence.

    And please, KF, don’t reply that expecting naturalistic causes for life is “extraordinary” without providing examples of established instances of supernatural causation of observed phenomena in this world.

  41. This illustrates the most important objection to ID. Not that it is proven wrong but that it short circuits curiosity and diminishes the desire to find natural regularities. The search for regularity is practically synonymous with science.

  42. kairosfocus loses focus:

    DrWho: “Kairosfocus hypothesises that non-living intelligent designers created the first life forms.

    kairosfocus: [g –> This is now so much of an insistent distortion in the teeth of repeated correction and duties of care to fairness and accuracy that it is a lie, a statement in willful disregard to the truth, hoping to profit by it being perceived as the truth.

    If “non-living” intelligent designers did NOT create life then it must have been “living” designers that created life.

    More circular thinking.


  43. Barry: “UD Editors:  No one has come close to refuting UB’s thesis after 129 comments.”

    Onlookers will notice that TSZ successfully refuted every claim he made.

  44. I forget. What was his thesis, other than infomation is always physically instantiated, that information transfer is always physical, and that translation is analogous to code deciphering? I don’t believe we refuted that so much as wondered what it had to do with ID.

    Unless it was the claim that since humans are the only known entities that have made codes, they must have made the genetic code. Or something like that. I can never follow that.

  45. His main focus seemed to be “recorded information” which begs the question, “Then who recorded that first information and how was it done?”

    He never said but he did dig himself a big hole in a wet lawn!


  46. UB make this “case” every so often.  I can never get beyond the first three steps (his text in italics, my response in plain).


    1. A representation is an arrangement of matter which evokes an effect within a system (e.g. written text, spoken words, pheromones, animal gestures, codes, sensory input, intracellular messengers, nucleotide sequences, etc, etc).

    This includes all sorts of different things – but let’s go with it and see what happens.

    2. It is not logically possible to transfer information (the form of a thing; a measured aspect, quality, or preference) in a material universe without using a representation instantiated in matter.

    False – although exactly when it is false depends on what is meant by a representation. Suppose I want to inform someone that badgers regularly visit my garden. I can transfer this information in many ways

    1) Writing them a letter telling them. This presumably falls into the category UB was expecting.

    2) Showing them a footprint. This shows them the size and shape of the feet and thus informs them about at least this aspect of the animal. If they have background knowledge they may be able to learn more. Does a footprint count as a representation?

    3) Getting them to observe the trail leading to a badger! Is the trail the representation?

    4) Getting them to come along one night and see the badgers. Not sure what counts as the representation here

    3. If that is true, and it surely must be, then several other things must logically follow. If there is now an arrangement of matter which contains a representation of form as a consequence of its own material arrangement, then that arrangement must be necessarily arbitrary to the thing it represents. In other words, if one thing is to represent another thing within a system, then it must be separate from the thing it represents. And if it is separate from it, then it cannot be anything but materially arbitrary to it (i.e. they cannot be the same thing).

    This is quite hard to understand. In my examples above the footprint and the trail are definitely seperate from the badger – but materially arbitrary? – I really don’t know what that means.

  47. Onlookers will notice that TSZ successfully refuted every claim he made.

    Indeed.  Barry needs to refine his statement to “No one we allow to comment here has bothered to refute UB’s thesis after 129 comments.”

    I’m trying not to give UD any additional traffic — has anyone bothered to reference the discussion here on those threads?

  48. That seems to be a problem with UPB’s argument. The more you clarify it the less there is. The more you weed out obviously absurd interpretations and examples, the less relevant it is to biology.

    It boils down to chicken and egg. You can’t have one without the other. Therefore Designer. All the verbiage is horsefeathers.

  49. Actually I think Barry is dissembling. Mphillips was well on the way to disemboweling UPB’s argument before KF’s warning and before Barry ditched the thread where mp had made some significant hits. This was a transparent effort to shove that down the memory hole.

    The fate of mphilips will remain one of those internet mysteries. I have a theory, but it will have to remain private.

  50. Joe: “Well TSZ claims to have refuted every one of UB’s claims. And if bald assertions, misrepresentations and nonsense were refutations they would have a point. “

    What about bald assertions of the existence of an intelligent designer?

    Do they count for your side?


  51. Upright Biped is reported as saying:’

    And if it is separate from it, then it cannot be anything but materially arbitrary to it (i.e. they cannot be the same thing).

    What a very curious – (and altogether wrong) use of the word “arbitrary” – which means “arrived at by free choice”

    It does not mean “separate”

    A badger’s tracks are anything but arbitrary. They are necessarily, and without choice, made by a badger – however far separated that badger may be from its tracks when they are seen.

    We can add the misuse of this word to that of “semiotic” and “protocol” in UB’s efforts.

    Come to think of it, he is assigning arbitrary meanings to these perfectly good words! – which is a thing to be avoided if one hopes to be understood

  52. Come to think of it, he is assigning arbitrary meanings to these perfectly good words! – which is a thing to be avoided if one hopes to be understood

    Cui bono?

  53. kairosfocus: “A claimed cause of a effect must have empirical support that it is adequate. No observation, no empirical support. KF “

    Do you have empirical support that the designer, ID’s claimed cause of life, had adequate ability to cause the effect we call life?

    Have you ever observed the designer at work?


  54. UPB’s misunderstanding:

    RB: May, 2012

    “I assert (not suggest) that you do not understand entailment, and due to your failure to grasp entailment you have constructed an argument beset with a fatal logical flaw.”

    UB: June, 2012

    “Bill, if a specific thing only exist under specific conditions, then does it existence entail the existence of those specific conditions? Or is that illogical?”

    RB: June, 2012:

    Yes, it does. So that would be a valid use of “entailment.” …”

    UPB should read more carefully.

    In May, RB refers to an *invalid* use of entailment.

    In June, UPB demonstrates a *valid* use of entailment, i.e., not the *invalid* one in his “semiotic theory” argument.

    RB, points out that the June statement is a *valid* use of entailment.

    This in no way implies a change in opinion by RB that his “semiotic theory” argument is now considered by RB to be *valid*.

    I too agreed that this June statement by UPB is *valid* and also still consider his “semiotic theory” argument is still logically flawed.


  55. Joe: “Hey Toronto- how do we know someone had the ability to build Stonehenge? Answer = Stonehenge! “

    Hey Joe, how do we know “no designer required evolution” would result in us? Answer = us!

    Joe’s logic is even easier to use than UPB’s!

  56. Joe:”It didn’t result in us as we are not the result, just another link and we are not alone on this planet. “

    We are the result of either ID or “no designer required evolution”.

    Logically, the cause of us is either A or (~A) where A = ID.


  57. UB’s choice of venue in which to (mis)characterize the course of our previous discussion here speaks for itself. 


  58. Joe: “You want to discuss how we know the abilities of designers and I told you. “

    No, you said your premise results in your conclusion.

    I responded that my premise results in my conclusion.

    You claim that’s not good enough.

    Okay then, we’ll set aside both our assertions and just focus on mechanisms.

    Our side has a mechanism that you say is lacking but your side is lacking a mechanism.

    That makes us the winners by default.


  59. Information. Hmmmm. I haven’t checked in with UD today, but my guess (if we aren’t talking of derails and jokes-that can’t-possibly-be-jokes) is that we are being invited to consider representations and instantiations and how the codon-acid mapping IS an informational relationship, not a chemical one …

    Given that the DNA-protein relationship takes place at the molecular level, just what IS information at this level? Molecules are collections of atoms that share an interest in charge. Protons and electrons attract. If an atom has spare space in its orbitals, it will share electrons with another. But atomic nuclei, being positive, repel each other. The result is a stable, lowest-energy arrangement, where nuclei sit as far away from each other as possible but get a slice of their electrons’ orbits. Nuclei like electrons, hate other nuclei. The result of these competing tensions is a 3D arrangement in space, with positive charges localised and negative charges somewhat more diffuse shuttling between them (and the charge pairs bouncing photons off each other all the while).

    What ‘information’ is there in this arrangement? It really depends what you are. If you are a neutrino, you can barely see atoms, and could pass right through the earth without knowing it is there. If you are a photon, you could bounce off matter or be absorbed by it. If you are matter, your interaction depends on whether or not you are charged. But in all cases, interaction means a change in energy. If you react chemically and spontaneously, you give off heat and adopt a lower energy configuration. If you interact physically, such as folding interactions in a newly synthesised protein, again you adopt the lowest accessible energy configuration and shed heat as you do so. Or you might just bump into matter, and interchange  kinetic energy. But: no interaction, no ‘information’. And it is all about what the interactors can ‘see’ – 3D orientation and charge density, mostly. 

    There isn’t really much else. At the molecular level, ‘information’ means interaction. So when people talk of a codon ‘representing’ an amino acid, or ‘informational (sequence) entropy’, I have no idea how to translate that into chemistry.

    A tRNA molecule is essentially an L shaped stick. An aaRS interacts with one end of the L. The charge densities and shape of the 3D structure behind the Acceptor stem determine whether a particular aaRS will interact with this tRNA or not. If it does, it glues a specific amino acid to it. In such manner, a set of charged tRNA molecules builds up – baited sticks. The other end of the stick has a triplet of bases – the anticodon. The ribosome passes along an mRNA strand and, for each triplet of bases, binds the tRNA with the strongest affinity for the currently exposed triplet (sometimes it is a tie). The winner docks, the amino acid is oriented against the growing peptide and is peptide bonded to it.

    But there is no meaningful sense in which the mRNA (or original DNA) represents the amino acid that ultimately gets put in place. It causes it, as part of a whole web of causation, but it does not represent it. One end of a stick does not represent the other symbolically, still less the hole that that end happens to fit.

  60. kairosfocus: “Similarly, it is not an unfair challenge to demand that a claimed causal factor held to be sufficient to cause an effect be demonstrated as actually doing so in our observation. That boils down to that in science — and common-sense day to day life — claims are subject to empirical observational tests. “

    Demonstrate that your design process can see the future “specific functionality” required for its designs.

    If you can’t, your designer is as blind in the search-space as “non-guided by an intelligence” evolution.


  61. KF:

    …demonstrated as actually doing so in our observation

    There is the extra difficulty for ID of demonstrating not only the capacity of their mechanism (if such it could be claimed to be) to produce the effect, but to do so when there is no complex physical substrate to contain it. If it can’t, it is a hopeless causal factor in explaining the generation of complex physical substrates. 

    But the matter of demonstrations is a red herring, from a purported despiser of these distractive fish. There are many phenomena that are not amenable to direct demonstration – nucleosynthesis in stars, the transition from massive star to black hole, galaxy formation, the existence of quarks, transistion to/from ice ages … for the historic phenomena, the ‘best inference’ cause, from oft-invoked Newton onwards, has been mechanisms reasonably inferred to have been available at the time in question.

  62. It is a puzzle how intelligence can help on a search of a space whose ‘fitness map’ is unknown. If there is any ‘information’ helping to guide the search, it is available to dumb processes as well as intelligent ones. Bury a few gold doubloons, eliminate anything that could be construed as a clue, then have one digger given co-ordinates at random, while the other applies his intelligence to the task. 

    If ‘being intelligent’ means knowing the map – knowing, for example, which peptides are functional and which are not at a given length in a given organism – that really is not the same phenomenon that they pointed to at the commencement of their chain of inference. They have smuggled something in.

  63. Kairosfocus:


    Of course, we see from Venter et al that it is reasonable to expect that a sufficiently sophisticated molecular nanotech lab can do a living cell. As as been repeatedly pointed out and insistently ignored.

    Certainly not ignored here on TSZ, (the place where people are allowed to say what they want!). In my last post, I agreed with KF that it’s very reasonable to suppose that humans will design life in the future. I also pointed out why that doesn’t justify the inference that humans (obviously) or unknown intelligent designers designed life as a best explanation. KF, we know that we can make things that are found undesigned in the wild. If you didn’t like my example of dammed rivers forming lakes, you could think of some things we make can make in the lab. Start where you want. Snowflakes, maybe?

    But even that is too much.

    The basic thing is that we have good reason to see the only observed cause of FSCO/I, and to see why the lottery to get to it by chance and blind mechanism will not be winnable. So, what we do is we look at a key signature in cell based life and infer that the known and reliably observed cause of such, design is the best explanation.

    Look at the first phrase of your first sentence. Your observed cause is human design, thus showing that A (humans) cannot be responsible for all B (FSCO/I), as FSCO/I, however you precisely define it, would be a prerequisite for our existence. You like to make abductive and inductive inferences, so here you’re missing an obvious induction. As FSCO/I is a prerequisite for the existence of all known intelligent designers, it is reasonable to infer that it is a prerequisite for all intelligent designers. Call that “dr. who’s law”. Your second phrase, about the unwinnable lottery, is an unsupported claim unless you can demonstrate that a non-telic OOL breaks laws of physics/chemistry. All of which means your second sentence is completely unsupported, and you clearly have no theory of I.D.! Not even a good hypothesis to build one on.

    Not hard, but rather inconvenient for those who wish to insist that that which has never been seen doing such, and which runs into a major sampling theory challenge to look like a credible winner of a lottery, is what “must” have happened.

    I wasn’t aware that non-living intelligent beings had been observed at all, let alone observed designing things, let alone observed designing FSCO/I without themselves containing or requiring it for their existence, let alone observed designing life. When I say things like the above, you, Kairosfocus, seem to think that they are metaphysical statements. They are not. Just observation about the world we’re in. Doesn’t it ever occur to you that pointing to the behaviour and abilities of living intelligent beings is an inherently faulty basis for making abductive inferences about the origins of the life system of which they are a part?

  64. kairosfocus: “[k –> As long as such evo is a search, and as long as it depends on chance for variations to be culled out by differential reproductive success, it is amenable to examination on the credibility of chance based trial and error search, and analysis on signs. “

    How does your designer get around the problems associated with your “search space”.

    Unless your designer can foresee the future, he also has to work with trial and error.

    If you claim that he already has working models of life that he can make small modifications to, then so does evolution.

    You need a designer who can reliably see the future to the point of making 100% reliable prophecies.

    Show the onlookers something with that capability.


  65. KF’s argument has always hinged on the concept of “isolated islands.” That and irreducibility. It’s the molecular equivalent of no intermediate fossils. And, of course, the ID advocates think the argument is airtight because there are no molecular fossils.

  66. On “broughtupcy”:

    I made a comment on Kairosfocus’s abductive reasoning further up the thread, which started our first exchange. He prefaced his first reply with this:

    Looks like Dr Who is trying for at least a bronze in the poster-child category:

    Which puzzled me slightly. Here’s my post:

    A comment on Kairosfocus’s abduction to arrive at a best explanation for the OOL.

    A is known to be a source of B

    No other source of B is known.

    Therefore, I infer that A is the best available explanation of any B.

    That kind of abduction seems to work well when A and B are specific well described things. Humans and written language, for example. If archaeologists discovered an ancient tablet with symbols that appeared to be writing, they could reasonably infer that humans were responsible. It’s not a proof. Aliens could conceivably have visited the planet and done some scribblings, for example, but humans are currently by far the best explanation.

    The above type of abduction is what Kairosfocus seems to believe he’s doing.

    But this is what Kairosfocus really does.

    A is known to be a source of B

    No other source of B is known

    Therefore, I infer that an unknown C which shares a property with A is the best explanation of any D which is similar or analogous to B, and could be given the same broad description.

    And he ends up with non-living intelligent designers, something not known to exist, as a best explanation for the origin of life.

    I looked at the top of the thread, and found that “poster child” meant I’d been highlighted as a poster child of illogic and want of civility:

    KF: Over the past several days, I have been highlighting poster children of illogic and want of civility that are too often found among critics to design theory

    This all seemed very odd. If someone is so concerned with civility, why would that person preface their first reply to me with what seemed to be name calling. After another post from me (completely devoid of name calling or insults), KF replied again, upgrading me from a bronze poster child to:


    Dr Who is today’s poster-child no 1, for this parody — he CANNOT have meant this seriously — of abductive reasoning (with a healthy dash of strawman false statement after repeated correction on the side):

    This, apparently, is an expression of the “broughtupcy” he encourages in others. Now, I suspect, I’ll no longer be replied to, having been conveniently categorized amongst the poster children. KF starts a post today with this:


    This morning, we are not dealing with a poster child of irresponsible and outrageous conduct….

    Which presumably means he’s not addressing those to whom he has recently been uncivil. Going by this experience of a first exchange with KF, I don’t really find it surprising that he attracts some genuinely “uncivil” comments. But I get the impression that he’s so lacking in self awareness that he can’t percieve his own very apparent lack of “broughtupcy”, as he puts it.

  67. Does that mean he took Umbridge at your post and elevated your status to Undesirable No.1?

    It is a bit uncivil to laugh at people when they have been unintentionally funny. So consider yourself warned. Stronger measures of correction to follow.

  68. Joe: “For all this blah, blah, blibbidy-blibbidy blah, no one has put forward any evidence that blind and undirected processes can produce the transcription/ translation system we observe in living organisms. And no one even knows how we could test such a premise. “

    No one has produced any evidence that an “intelligent designer” can get around the “search space” problem unless he knows what to design for an unseen future.

    KF says “designed” life can adapt itself just as evolutionists said it does.

    KF says evolution has nothing to say about the OOL, just as evolutionists have always said.

    Looks like we don’t have a problem anymore.

    Teach “unguided by an intelligent designer” evolution in schools and teach your ID theory about the OOL in Sunday School where it belongs.


  69. Hmmm … I’ve been ‘corrected’. Me and my stupid degree in the subject an’all! And my job as a code-monkey!


    OK Allan, just because there is a lionk-up between the tRNA and the codon (in the ribosome) does NOT mean there is a physio-chemical connection between the codon and the amino acid. As UD said the relationship is arbitrary which means there isn’t any law that determines it- the choice of amino acid to specific codon.
    Joe, AM needs to observe the discussion and diagram here at Wiki, and to understand that the CCA-coupler that carries the AA is a standard bloc. It is the loading enzyme that “recognises” a given tRNA and loads it with the correct AA. Indeed, this has been used to load tRNA’s with artificial AA’s and used onwards to create new, unnatural proteins. In short the connexion USES the standard chemistry, but the AA for a given tRNA with a given anticodon is assigned on an INFORMATIONAL basis not a chemical basis. The transcription-translation protein synthesis process USES chemistry but is not driven by blindly forced chemical interactions. Instead, the crucial step is plainly informational, i.e a given codon tells the tRNA entering the Ribosome and coupling to it, to couple the loaded AA as the next in the chain. Then the Ribosome ratchets the mRNA tape forward one slot, and the next tRNA is used to add, until the stop codon comes along.

    Approximately right on the detail but a confusion of categories of interaction. Sticking in words like ‘recognises’, ‘tells’, even ‘informational’ are just anthopomorphisations that assist in conveying the essence of the process to laymen or students. Nothing ‘tells’ tRNA to snuggle up to the growing peptide – certainly not the currently exposed codon. It is driven there by energy – gradients and binding affinity. 

    It does not matter a hoot if a different acid can be attached to the ACC stem. The mechanism by which you alter aaRS activity is by messing with the physics of the system – by retooling ACC-stem bases, aaRS binding site or anticodon such that binding affinities for tRNAs or acids are redrawn. Which, of course, a human genetic engineer can do, completely non-controversially.

    The ‘law-bound’, chemical nature of this system is not waved away simply because the two ends of tRNA are independent (another way of presenting the ‘arbitrary’ case, ie codon XXX does not lead with chemical inevitability to acid A). tRNA acts more-or-less like a bent stick with two ends, having spontaneously (exothermically) folded from its primary sequence by physical interaction between its atoms. One end binds with one chemical arrangement, the other with another – the aaRS binding site and mRNA respectively. Both interactions are entirely physico-chemical, and ‘informatic’ only in the sense that all of chemistry is – molecular ‘information’ is solely the spatial distributions of atoms and charges, and the energies of interaction that generate forces between them. To say that an interactor binding to some of the atoms at one end semiotically ‘symbolises’ a molecule brought in by one binding to some atoms at the other stretches the category ‘symbol’ well beyond breaking point.  

    This is an informationally controlled, algorithmic, coded, step by step process. KF

    It is controlled, in that the energy of the serial transitions is not released all at once. It is step by step in the same sense. It’s algorithmic in that there are a series of actions which (given that they follow the laws of physics) will operate with reasonable fidelity. But ‘coded’? In what way? What makes the the physical independence of the two ends of tRNA into a symbolic code, or the following of thermodynamic gradients a trick requiring programming? You don’t have to program an electron to be attracted to a proton, nor does it need any ‘information’ beyond the Coulombic field.

  70. In fact – to short-cut the guff – it is precisely the independence of the two ends of tRNA (the so-called ‘arbitrariness’) – that allows the possibility of protein synthesis evolution, from a minimal-acid system to a multiple, and from a few-codon system to 61, without the simultaneous changes that would be demanded if coupling were tighter.

  71. And what they’re all fighting shy of saying is, that for all their use of bastardised meanings of words like “semiotic”, arbitrary”, and “protocol”, they absolutely believe that the codon triplets were arbitrarily (sensu stricto) assigned to amino acids.

    By an Assignor/Designer/god.

    In other words, they are assuming their conclusion – plus of course using the old “can’t see how that could have happened in nature, must have been designed” trope.

    Who’d a’ thunk it? 

  72. kairosfocus: “4: Is it therefore reasonable to identify that functionally specific complex organisation and/or associated information (FSCO/I, the relevant part of Complex Specified Information as identified by Orgel and Wicken et al. and as later quantified by Dembski et al) is – on a broad observational base – a reliable sign of design? Why or why not? “

    Definitely NOT a reliable sign of design.

    How do you know what “specific functionality” is required for a future that hasn’t arrived yet?

    Is the designer someone who can see into the future?


  73. I remain appalled that kairosfocus can continue to use the terms FSCO/I and “Complex Specified Information” as if they had referents in reality when he has never been able to define them rigorously or show how to calculate them.  Until he can do so, using those terms simply emphasizes his intellectual dishonesty.

  74. I note that Shapiro, for all the interest he generates in folks like UPB, denies that his “natural engineers” can forsee need.

  75. Joe: ” And we are appalled that Patrick/ MathGrrl can still insist that FCSO/I has not been rigorously defined when in fact it is more rigorously defined and measured than anything his position has to offer.

    I take he is is still upset that his position has nothing.”

    How do you know what “specific functionality” will be required in a yet unknown future?

    Does the “designer” have powers that are not bound by physics or is he just a materialist who knows the future can only unfold in one way?


  76. So Joe is still lurking about, hoping for an opportunity to demonstrate his rhetorical skills by posting more links to genitalia?

    Did he actually post a rigorous mathematical definition of kairosfocus’ metric and some example calculations or did he just, as per usual, claim to have done so without providing any evidence?

  77. What bothers me is that they’ve never assigned a weight to any of their values.

    For instance, does a human eye have a complexity of 1.6, a functionality of 1.2 and a specification of 1.8.

    What about an octopus or insect’s eye?

    Are they less complex but more specific?

    How do you measure that?

    If all we care about is that the description exceeds 500 bits, why bother with the other terms?


  78. Joe:”You write a GA to allow for “built-in responses to environmental cues”. “

    Then your UPB is useless as a metric if you’re willing to accept that the environment can drive evolution to solve fitness problems as they arise.


  79. kairosfocus: “I have seen absolutely no reason to reconsider my utter lack of interest in commenting at TSZ. The fundamental problem there being selective hyperskepticism. The rhetorical antics of several objectors to design theory there deserve iconic status as poster-children for irresponsibility on serious matters. “

    I wonder what would happen in a Dover-like trial. Would kairosfocus just fold and walk away because his feelings were hurt when the evolution side said, “We think you’re wrong”?


  80. Joe: “YOU need POSITIVE evidence and all you have are bald declarations. “

    I have never met or heard of anyone walking into a lab, putting some chemicals together and designing life.

    Show me some positive evidence that such a person exists and has those capabilities.


  81. It warms my little heart thinking of a Dover trial with Dembski, Joe, BA77, and KF witnessing (so to speak) for ID.

    I proudly hold the badges of first Poster Child and first Undesirable Number One. As for my seriousness, during the Weasel debates I took the trouble to learn a bit and invent my own GA that does not have an explicit target. Just to improve my own understanding.

    I believe there was an ID supporter who did the same thing, and I have wondered why he stopped posting. He seems to have been the first on the ID side to disagree with KF and Dembski.

  82. Ah, you don’t need POSITIVE evidence when you can make inferences…

    The bottom line is mutual incredulity. ‘Nature’, undirected, cannot achieve a certain kind of complexity (says one). ‘Design’ certainly can’t, since it is only manifest in entities with that very kind of complexity (says the other).

  83. To see that there remains a problem for evolution in all this, we need to look more closely at the connection between search and information and how these concepts figure into a precise formulation of conservation of information. Once we have done this, we’ll return to the Miller-type examples of evolution to see why evolutionary processes do not, and indeed cannot, create the information needed by biological systems. Most biological configuration spaces are so large and the targets they present are so small that blind search (which ultimately, on materialist principles, reduces to the jostling of life’s molecular constituents through forces of attraction and repulsion) is highly unlikely to succeed. As a consequence, some alternative search is required if the target is to stand a reasonable chance of being located. Evolutionary processes driven by natural selection constitute such an alternative search. Yes, they do a much better job than blind search. But at a cost — an informational cost, a cost these processes have to pay but which they are incapable of earning on their own.

    This seems to be the keystone of Dembski’sID argument from incredulity.

    Unfortunately for him, the very experiments he cites support evolution doing a blind exhaustive “search.” Lenski says this explicitly.

  84. Selective hyperskepticism? What a cheek! That is the UD stock-in-trade. Unless someone can point to a piece where they congratulate a ‘Darwinist’ for getting something right. And as for rhetorical antics …

    I do wonder who among the UD regulars would submit to cross-examination at a Dover ll. And, for any who might, who among their peers would want them to. I actually think Joe might be up for it, given his apparent belief that he can correct geneticists on genetics, programmers on programming, physicists on physics, chemists on chemistry …

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