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At Evolution News: Rosenhouse’s Whoppers: The Environment as a Source of Information

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William Dembski writes:

I am responding again to Jason Rosenhouse about his book The Failures of Mathematical Anti-Evolutionism. See my earlier posts here and here.

In Rosenhouse’s book, he claims that “natural selection serves as a conduit for transmitting environmental information into the genomes of organisms.” (p. 215) I addressed this claim briefly in my review, indicating that conservation of information shows it to be incomplete and inadequate, but essentially I referred him to technical work by me and colleagues on the topic. In his reply, he remains, as always, unpersuaded. So let me here give another go at explaining the role of the environment as a source of information for Darwinian evolution. As throughout this response, I’m addressing the unwashed middle.

Darwinian evolution depends on selection, variation, and replication working within an environment. How selection, variation, and replication play out, however, depends on the particulars of the environment. Take a simple example, one that Rosenhouse finds deeply convincing and emblematic for biological evolution, namely, Richard Dawkins’s famous METHINKS IT IS LIKE A WEASEL simulation (pp. 192–194 of Rosenhouse’s book). Dawkins imagines an environment consisting of sequences of 28 letters and spaces, random variations of those letters, and a fitness function that rewards sequences to the degree that they are close to (i.e., share letters with) the target sequence METHINKS IT IS LIKE A WEASEL. 

So What’s the Problem?

The problem is not with the letter sequences, their randomization, or even the activity of a fitness function in guiding such an evolutionary process, but the very choice of fitness function. Why did the environment happen to fixate on METHINKS IT IS LIKE A WEASEL and make evolution drive toward that sequence? Why not a totally random sequence? The whole point of this example is to suggest that evolution can produce something design-like (a meaningful phrase, in this case, from Shakespeare’s Hamlet) without the need for actual design. But most fitness functions would evolve toward random sequences of letters and spaces. So what’s the difference maker in the choice of fitness? If you will, what selects the fitness function that then selects for fitness in the evolutionary process? Well, leaving aside some sort of interventional design (and not all design needs to be interventional), it’s got to be the environment. 

But that’s the problem. What renders one environment an interesting source of evolutionary change given selection, variation, and replication but others uninteresting? Most environments, in fact, don’t lead to any interesting form of evolution. Consider Sol Spiegelman’s work on the evolution of polynucleotides in a replicase environment. One thing that makes real world biological evolution interesting, assuming it actually happens, is that it increases information in the items that are undergoing evolution. Yet Spiegelman demonstrated that even with selection, variation, and replication in play, information steadily decreased over the course of his experiment. Brian Goodwin, in his summary of Spiegelman’s work, highlights this point (How the Leopard Changed Its Spots, pp. 35–36):

In a classic experiment, Spiegelman in 1967 showed what happens to a molecular replicating system in a test tube, without any cellular organization around it. The replicating molecules (the nucleic acid templates) require an energy source, building blocks (i.e., nucleotide bases), and an enzyme to help the polymerization process that is involved in self-copying of the templates. Then away it goes, making more copies of the specific nucleotide sequences that define the initial templates. But the interesting result was that these initial templates did not stay the same; they were not accurately copied. They got shorter and shorter until they reached the minimal size compatible with the sequence retaining self-copying properties. And as they got shorter, the copying process went faster. So what happened with natural selection in a test tube: the shorter templates that copied themselves faster became more numerous, while the larger ones were gradually eliminated. This looks like Darwinian evolution in a test tube. But the interesting result was that this evolution went one way: toward greater simplicity.

Simple and Yet Profound

At issue here is a simple and yet profound point of logic that continually seems to elude Darwinists as they are urged to come to terms with how it can be that the environment is able to bring about the information that leads to any interesting form of evolution. And just to be clear, what makes evolution interesting is that it purports to build all the nifty biological systems that we see around us. But most forms of evolution, whether in a biology lab or on a computer mainframe, build nothing interesting. 

The logical point at issue here is one the philosopher John Stuart Mill described back in the 19th century. He called it the “method of difference” and laid it out in his System of Logic. According to this method, to discover which of a set of circumstances is responsible for an observed difference in outcomes requires identifying a circumstance that is present when the outcome occurs and absent when it doesn’t occur. An immediate corollary of this method is that common circumstances cannot explain a difference in outcomes

So if selection, variation, and replication operating within an environment can produce wildly different types of evolution (information increasing, information decreasing, interesting, uninteresting, engineering like, organismic like, etc.), then something else besides these factors needs to be in play. Conservation of information says that the difference maker is information built into the environment. 

In any case, the method of difference shows that such information cannot be reducible to Darwinian processes, which is to say, to selection, variation, and replication (because these are common to all forms of Darwinian evolution). Darwinists, needless to say, don’t like that conclusion. But they are nonetheless stuck with it. The logic is airtight and it means that their theory is fundamentally incomplete. For more on this, see my article with Bob Marks titled “Life’s Conservation Law” (especially section 8). 

Evolution News

Dembski’s conclusions are consistent with expectations from information theory and the generalized 2nd law of thermodynamics; namely, that natural processes cause a system to lose information over the passage of time. If an increase in information is seen in any system (such as life from non-life, or the appearance of novel, functional body plans or physiological systems), then natural processes cannot have been the cause. If not natural, then the increase in information must have come from an intelligent agent (the only known source of functional information).

107 Replies to “At Evolution News: Rosenhouse’s Whoppers: The Environment as a Source of Information

  1. 1
    Alan Fox says:

    The environment is a source of information. It is the non-random information that selection feeds on.

  2. 2
    Alan Fox says:

    In Rosenhouse’s book, he claims that “natural selection serves as a conduit for transmitting environmental information into the genomes of organisms.” (p. 215)

    Exactly.

  3. 3
    relatd says:

    AF at 1,

    The environment provides exactly what kind of information? To make a novel organ? Or body plan?

    AF at 2,

    Exactly? Exactly what?

  4. 4
    Alan Fox says:

    Exactly? Exactly what?

    Exactly what Jason Rosenhouse wrote. To assist you, I quoted it.

  5. 5
    relatd says:

    The environment provides exactly what kind of information? To make a novel organ? Or body plan?

  6. 6
    Alan Fox says:

    The environment provides exactly what kind of information? To make a novel organ? Or body plan?

    Organs and bodyplans are never new. We humans are doughnuts with excrescences, topologically speaking. (Look up deuterostomes if you don’t believe me).

  7. 7
    relatd says:

    I don’t believe your claims. Everything happened through accidents followed by more accidents involving a process with no goals. Baloney.

  8. 8
    asauber says:

    “Organs and bodyplans are never new.:

    AF,

    They were new at one time.

    Andrew

  9. 9
    OldArmy94 says:

    Alan Fox: All empirical observations of evolutionary processes indicate that information is lost, never gained. Antibacterial resistance? Loss of information. Polar bears? Loss of information.

    And so forth. There is no magic repository of environmental information waiting for evolution to open and pull out goodies.

  10. 10
    relatd says:

    Evolution does whatever it wants whenever it wants and has no goals. It is incapable of long-term planning. The “environment” had better have the right food, the right weather and the right type of shelter – right now. The fiction that some environment somewhere just happens to be the right fit is fiction. A made up story. An organism is born in the wrong environment and the right environment is hundreds of miles away or a change of season triggers a mass migration. How did the birds, for example, know where to go? Nobody/Evolution gave them a map? They got there by accident? Every year?

    https://earthsky.org/earth/which-bird-migrates-the-farthest/

  11. 11
    Red Reader says:

    “At issue here is a simple and yet profound point of logic that continually seems to elude Darwinists…”
    Ultimately, everyone chooses what they want to believe and Darwinists choose to believe “something comes from nothing” even though there is no evidence of this in the real world of cause of an effect, thermodynamics, and E=mc2.
    Something coming from nothing can’t even be imagined for as soon as one imagines something from nothing, one’s brain begins to imagine that “nothing” really is “something”: a “law”, a “force”, a fluctuation, a chance, a green fairy…really anything but an Intelligent Creator will do.
    It’s not that the logic eludes them, it’s that their mind is made up and their eyes are shut to the evidence all around them: “We don’t know how it all started and may never know, but we’re sure it wasn’t God.”

  12. 12
    Alan Fox says:

    They [organs and body plans] were new at one time.

    Not really. All the heavy lifting is done in the first two billion (that’s two thousand million) years of evolution following the emergence of life on Earth. Once you have eukaryotic cells, sex and multicellularity, it becomes a question of regulatory genes, gene switches, HOX genes. Look up Evo-devo (evolutionary developmental biology).

  13. 13
    relatd says:

    AF at 12,

    Here’s the formula: Life starts, a mindless process accidentally adds modifications, plus billions of years.

    Not even a joke, just a magical curtain that hides the way anything really happened regarding the development of life. Not credible at all.

    Regulatory genes magically appear and “know” how to function.

    Gene switches also have the correct function, again, by magic.

    HOX genes also know how to fit right in.

    To all reading. We are being presented with a magic formula. A formula where blind, unguided chance builds complex living things by magic.

    Not credible.

  14. 14
    Alan Fox says:

    Forgot the niche again. Remember the niche, Leto, remember the niche.

  15. 15
    relatd says:

    Tonight on The Niche, Alan Fox uses his magic curtain to modify a living thing over a million years! Really! Trust us! It happened – and uh… no one saw it happen but uh… somehow, maybe…

  16. 16
    Caspian says:

    AF @ 1:
    Like many others, you correctly surmise that the environment is a source of information, but unfortunately for evolutionary hopefuls, it is a woefully insufficient source of information. The non-living environment of the entire earth doesn’t have enough information, even if in a counterfactual world it could all be concentrated into one reaction, to construct one bio-relevant protein, let alone an entire cell. This impotency of nature to generate functionally complex systems, is why we see evidence for intelligent design as the explanation for living things. Why is this apparently so hard to accept?

  17. 17
    relatd says:

    Caspian at 16,

    Why is it so hard to accept?

    Here are the alternatives:

    1) Evolution through blind, unguided forces made all living things.

    2) An Intelligent Designer designed all living things.

    1) Is perfectly suited to the atheist.

    2) Is not suited. It can’t be accepted – ever. Admitting that living things are designed would overthrow the atheist view that all life, including human beings, appeared by accident.

    ‘Richard Dawkins once said, “Biology is the study of complicated things that give the appearance of having been designed for a purpose.” (The Blind Watchmaker, 1996, p. 1)’

    Question: Do flowers and birds and dogs appear to be the end result of chance? Of blind, unguided forces?

  18. 18
    Alan Fox says:

    This impotency of nature to generate functionally complex systems, is why we see evidence for intelligent design as the explanation for living things. Why is this apparently so hard to accept?

    I’m not convinced by the Sherlock Holmes fallacy. When eliminating unsatisfactory explanations and arriving at the default, you have to be sure you haven’t overlooked anything. Sure, evolution is an incomplete explanation and there may be better explanations that improve on or replace evolutionary theory. But (I keep saying this) “Intelligent Design” either explains everything or nothing. It’s untestable. It can’t simply be there just because other explanations are deemed inadequate.

  19. 19
    Alan Fox says:

    Do flowers and birds and dogs appear to be the end result of chance?

    Remember the niche. The bias that fuels selection.

  20. 20
    Seversky says:

    Caspian/16

    Like many others, you correctly surmise that the environment is a source of information, but unfortunately for evolutionary hopefuls, it is a woefully insufficient source of information.

    What exactly is this information and how is it quantified such that you can assert there isn’t enough of it in the terrestrial environment to account for life on Earth? We’re all talking about “information” as if it is a univocal concept and we’re all agreed on its meaning. Except we aren’t.

    And, if Dembski’s proposed conservation law of information means that it can neither be created nor destroyed then it must have always existed, which rather obviates the need for a Creator.

    I also think it’s unlikely you will find anyone in biology who commits the Hoyle fallacy of claiming that complex modern organisms sprang into existence in a single bound from simple, inanimate precursors. The claim is that modern organisms are the latest stage in a long evolutionary pathway made of small, incremental steps, most of which have not been captured in the fossil record. The lack of such evidence is obviously unsatisfactory but we have to make do with what we have and, spotty as it is, it is still more then we have to support the proposal of an extraterrestrial Intelligent Designer.

  21. 21
    kairosfocus says:

    AF, as usual, to object and toss out assertions of fallacy you provided yet another example of the known, reliable source of FSCO/I, intelligently directed configuration. Trillions of cases in point. KF

  22. 22
    kairosfocus says:

    Sev, explain please, the coded algorithmic information in D/RNA, antecedent to cellular metabolism and replication. Make reference to Newton’s rule to control unfettered speculation, alleged causes must have good observational support for their claimed causal power. KF

  23. 23
    Alan Fox says:

    AF, as usual, to object and toss out assertions of fallacy you provided yet another example of the known, reliable source of FSCO/I, intelligently directed configuration. Trillions of cases in point. KF

    You know full well what I think of your “FSCO/I”. Repetition won’t change my opinion. Only a demonstration of how you measure it might cause me to re-examine.

  24. 24
    Alan Fox says:

    Sev, explain please, the coded algorithmic information in D/RNA, antecedent to cellular metabolism and replication.

    It seems endemic among ID proponents here to ask questions they themselves can’t be answer, no matter how they load them.

    Algorithmic! Good grief.

  25. 25
    kairosfocus says:

    AF, first you know I only provided a summary phrase for an observable phenomenon highlighted by Orgel and Wicken in the 70s. Second, to object you provided yet another case in point. Third, your attempt to dismiss the point that FSCO/I is found in D/RNA has collapsed. Fourth, you are trying the Alinsky tactic, personalisation and polarisation; fail. KF

  26. 26
    kairosfocus says:

    PS, Orgel

    living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity . . . .

    [HT, Mung, fr. p. 190 & 196:]

    These vague idea can be made more precise by introducing the idea of information. Roughly speaking, the information content of a structure is the minimum number of instructions needed to specify the structure.

    [–> this is of course equivalent to the string of yes/no questions required to specify the relevant J S Wicken “wiring diagram” for the set of functional states, T, in the much larger space of possible clumped or scattered configurations, W, as Dembski would go on to define in NFL in 2002, also cf here,

    here and

    here

    — (with here on self-moved agents as designing causes).]

    One can see intuitively that many instructions are needed to specify a complex structure. [–> so if the q’s to be answered are Y/N, the chain length is an information measure that indicates complexity in bits . . . ] On the other hand a simple repeating structure can be specified in rather few instructions.  [–> do once and repeat over and over in a loop . . . ] Complex but random structures, by definition, need hardly be specified at all . . . . Paley was right to emphasize the need for special explanations of the existence of objects with high information content, for they cannot be formed in nonevolutionary, inorganic processes [–> Orgel had high hopes for what Chem evo and body-plan evo could do by way of info generation beyond the FSCO/I threshold, 500 – 1,000 bits.] [The Origins of Life (John Wiley, 1973), p. 189, p. 190, p. 196.]

    Wicken

    ‘Organized’systems are to be carefully distinguished from ‘ordered’ systems. Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions and/or repetitive stepwise procedures] and therefore lack complexity, organized systems must be assembled element by element according to an [ –> originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65. (Emphases and notes added. Nb: “originally” is added to highlight that for self-replicating systems, the blue print can be built-in.)]

  27. 27
    David P says:

    “So if selection, variation, and replication operating within an environment can produce wildly different types of evolution… then something else besides these factors needs to be in play.”
    In other words, selection, variation, and replication can be compared to a gambler’s method for picking winners at a horse race involving a certain set of circumstances.
    Some races this method picks a winner, other races it picks a loser. Whether the gambler likes it or not, some other set of circumstances is at play for determining which horse wins, not his.

    If we apply John Stuart Mill’s method of difference to convergent evolution and divergent evolution we have to admit some factor besides selection, variation, and replication is at play.
    This is the white elephant in the room and the main thrust of the article.
    It points out a fatal flaw in Darwinists logic.

  28. 28
    Alan Fox says:

    @ David P

    Something is missing from your analogy. You only breed from race winners. That is artificial selection. The horse genome already had variation. Selective breeding puts that into new combinations and the niche environment (of which the crucial element is the breeder) designs winning racehorses.

  29. 29
    jerry says:

    Selective breeding puts that into new combinations and the niche environment (of which the crucial element is the breeder) designs winning racehorses

    This is genetics and is incapable of producing anything but a horse.

    Natural selection obviously did not work in humans to produce a more productive human. For hundreds of thousands of years and tens of thousands of generations, the main characteristic for survival did not develop. That was strength.

    Strength was needed to make food more available/accessible and would have left more offspring. But it didn’t happen. Why?

    There is no example of natural selection producing anything really useful. Maybe a hyper imagination?

    Natural selection is self refuting as a generator of novelty/new characteristics. If it actually generated anything but trivial changes it would destroy the ecology within which the modified species existed and thus, the modified species itself.

    Logic and evidence are the enemy of the niche fantasy.

    Of course there is apparently a niche on UD for nonsense as it is well received by most ID commenters. What would they do if they couldn’t repeat the same replies over and over again.

    Let’s hear it for the nonsense niche.

  30. 30
    JVL says:

    Alan Fox: Only a demonstration of how you measure it might cause me to re-examine.

    Jeeze Alan, haven’t you learnt anything? They know it when they see it. After all these years . . .

  31. 31
    asauber says:

    “All the heavy lifting is done in the first two billion (that’s two thousand million) years of evolution following the emergence of life on Earth.”

    AF,

    Conveniently, no evidence of any heavy lifting exists from this Magical Era.

    Andrew

  32. 32
    kairosfocus says:

    JVL & AF, you have convinced us that you will refuse to acknowledge even observed facts. In the case of FSCO/I or its superset CSI, it is clear that you have closed your mind to the realities of a world where a few days ago I transferred 32 GB from documents to an SD Card with 50+ GB of ullage to free up a solid state drive. You have painted yourselves into a corner where the routine measurement of observably functionally specific bits of information has vanished into an artificial ideological blind spot driven by selective hyperskepticism. That tells us all we need to know about what is going on, especially where you AF are either implicated in gross and stubborn ignorance on coded D/RNA or tried to run a cynically deceitful bluff and brazen it out rhetorical stunt designed to gull your own supporters. I suggest, some rethinking is in order. KF

  33. 33
    jerry says:

    On cue, nonsense niche generates more nonsense.

    Will it lead to the devolution of UD? My prediction: destroy the nonsense gene or it will destroy UD. Maybe natural selection works and a more productive discussion site will emerge in another species.

  34. 34
    kairosfocus says:

    Jerry, I need say nothing more on niche, design being a misnomer. Such is incapable of intelligently directed configuration. Designer substitute? Not unless it can be empirically shown capable of creating 500 – 1,000+ bits of FSCO/I. The rhetoric games are because that is not in prospect. The rhetorical stunt on code in D/RNA just exposes the hyperskepticism we see from the penumbra of objectors. KF

  35. 35
    JVL says:

    Kairosfocus: You have painted yourselves into a corner where the routine measurement of observably functionally specific bits of information has vanished into an artificial ideological blind spot driven by selective hyperskepticism.

    No, as usual, you misrepresent our views. We don’t deny the existence of human created information. We just want to know how (in the case of biological systems for example) you determine if functional, complex, specified information is present AND how you measure how much there is.

    Is the whole human genome functional, complex, specified information? (About 3.1 GB of base pairs.) Is the whole marbled lungfish genome functional, complex, specified information? (About 130 GB of base pairs.) How about the genome of Tetraodon nigroviridis, a type of puffer fish at 390 MB of base pairs? That’s quite a variation just among vertebrates. Are marbled lungfish that much more ‘complex’ than puffer fish? If part of the marbled lungfish genome is not functional then can you figure out how much is?

  36. 36
    relatd says:

    Seversky at 20,

    Your worldview distorts your thinking. No one is proposing an extraterrestrial designer, except you. The obvious designer is God, not some unknown alien being.

    I think you understand ID but you try to create very unconvincing arguments against it.

    So Seversky, are you the result of a long evolutionary process? An accident?

  37. 37
    relatd says:

    JVL at 35,

    Yes, it’s all functional, all of it.

  38. 38
    David P says:

    @Alan Fox Perhaps my analogy should have used a roulette wheel, race cars, or plinko game. It isn’t about the winning horse so much as it was about the gamblers method to pick them. His method to pick winners actually picks both winners and losers. Therefore the set of circumstances his method relies on cannot be responsible.

    If selection, variation, and replication produce both information increasing and decreasing then this “set of circumstances cannot be responsible for the observed difference.”
    Another set of circumstances, circumstances that are “present when the outcome occurs and absent when it doesn’t occur” is required to produce information.

  39. 39
    asauber says:

    AF,

    David P just cleaned your niche clock.

    Andrew

  40. 40
    David P says:

    Just to make it clearer:
    If a gamblers method picks both winners and losers – that’s a really crappy method.
    According to Rosenhouse selection, variation, and replication explain both an increase and decrease information.
    How is that not a flawed method?

    Or these:
    selection, variation, and replication accounts for both change and stasis.
    selection, variation, and replication accounts for both adaptation and fixation.
    selection, variation, and replication accounts for both divergent and convergent evolution.
    selection, variation, and replication accounts for both….

  41. 41
    chuckdarwin says:

    I think Dembski and Rosenhouse should be banished to Thunderdome where the two math geeks can decide this nonsense once and for all. Myself, I’m getting sick of Dembski’s whining that no one understands him–It’s such a lame DI rag…..

  42. 42
    kairosfocus says:

    JVL, confession by projection. The method used has been reduced to a flowchart [per aspect . . .], laid out in steps, given as cases, specified as to threshold of 500 – 1,000 bits of FSCO/i. The pretended objection that it is subjective or unrecognisable is answered by the fact that to communicate objections you compose text in English rather than typical random typing gibberishbdrgj3e5tikyyejjrujh or empty repetition sdsdsdsdsdsd — and that has been on the table since Orgel and Wicken, it isn’t even a result of ID theory, it is an antecedent of the theory. We all know better, you know better, it is high time for you to do better. KF

  43. 43
    relatd says:

    CD at 41,

    Chuckdarwin has spoken !

    I’m sure Dembski did not hear you…

  44. 44
    relatd says:

    David P at 40,

    You are missing the simple formula: Anything explains everything in evolution.

    Evolution is fast except when it’s slow.

    Evolution makes a lot of changes except when it doesn’t. Take a fish called the coelacanth. It hasn’t changed in millions of years. Fossils show the exact same fish.

    The earth has gone through CATASTROPHIC changes over millions of years. You know, asteroid strikes, things like that. Really? How about an extinct tree that had gone missing for millions of years? You can buy immature plants right now. It’s called the Wollemi Pine. It was found growing in the wild in 1994.

  45. 45
    Alan Fox says:

    If selection, variation, and replication produce both information increasing and decreasing then this “set of circumstances cannot be responsible for the observed difference.”

    I was just trying to help improve your analogy to something closer to what I assumed you intended, an analogy for evolution, where successive rounds of variation and selection result in adaptive change.

    In that improvement, winning racehorses get to leave progeny, losing racehorses don’t.

    If you’d rather have an analogy that doesn’t have anything to do with evolution, you’re managing fine as you are.

  46. 46
    JVL says:

    Relatd: Yes, it’s all functional, all of it.

    Why does a marbled lungfish need a genome of 130 GB of base pairs whereas humans only need 3.1 GB of base pairs?

    Considering that ID is a better explanation.

  47. 47
    JVL says:

    Kairosfocus: specified as to threshold of 500 – 1,000 bits of FSCO/i.

    How do you know when you’ve hit that threshold? How do you measure FSCO/I?

    We all know better, you know better, it is high time for you to do better.

    Just spell out your methodology for detecting and measuring FSCO/I. Why won’t you do that?

  48. 48
    Alan Fox says:

    Just spell out your methodology for detecting and measuring FSCO/I. Why won’t you do that?

    I dunno. Maybe he can’t.

  49. 49
    kairosfocus says:

    JVL, did you see what I did a few days ago? Start by looking at the file structure on your PC. Your hyperskeptical attitude is no\w self referentially absurd, you use technology to object that pivots on measuring FSCO/I. KF

  50. 50
    Alan Fox says:

    Wollemia? Let’s fact check.

    Wollemia nobilisis a highly endangered species of tree recently found growing in a remote corner of New South Wales. It has no close living relatives and is considered more closely related to known fossil species. As always, there is nuance to the story that doesn’t get reported.

    https://en.m.wikipedia.org/wiki/Wollemia

    ETA there’s a detailed description of the phylogenetic analysis that shows the relatedness to other species, living and extinct.

  51. 51
    JVL says:

    Kairosfocus: did you see what I did a few days ago? Start by looking at the file structure on your PC. Your hyperskeptical attitude is no\w self referentially absurd, you use technology to object that pivots on measuring FSCO/I.

    Look, just spell out your methodology. Computer file structure is not at all the same as biological structures.

    Just spell it out. Stop ducking and dodging. Just spell it out.

  52. 52
    Alan Fox says:

    JVL, did you see what I did a few days ago?

    Did you calculate the FSCO/I of something?

  53. 53
    Lieutenant Commander Data says:

    marbled lungfish need a genome of 130 GB

    😆 Better keep quiet about because that is a big problem for darwinism. If darwinism would be true the genome start small (with prokaryotes) and grow with small steps( new functions and systems ) toward the most complex creatures (humans) . This is not the case.
    Genomes List

  54. 54
    JVL says:

    LtComData: If darwinism would be true the genome start small (with prokaryotes) and grow with small steps( new functions and systems ) toward the most complex creatures (humans) . This is not the case.

    I’d love to hear your explanation of why the marbled lungfish has a genome more than 40 times the size of the human genome.

    Are you here to provide scientific reasoning or just to throw doubt about?

  55. 55
    kairosfocus says:

    JVL, you full well know, stop hyperskeptically pretending it has not been on the table; beyond a point such is not innocent ignorance, but willful denial of facts. For record, the core logic is abductive inference to best explanation on tested reliable sign, first discussed on record by Hippocrates of Kos. As you further know, since Plato, with slight refinement, we explain on natural [= blind chance and/or necessity] vs the ART-ificial, i.e. intelligently designed configuration to an end. Notice, the common strawman on vs supernatural thence god of gaps, is just that, a strawman caricature. Notice too, process not agent, whodunit or howtweredun are onward investigations. There is therefore a double default causal inference, chance and/or lawlike necessity. Further, there is the question, are there reliable signs of ART, yes: start with FSCO/I, include irreducible complexity under the Menuge factors C1 – 5, go on to active information that puts you on a shoreline of function. Language expressed as complex text, especially algorithms [so, goal directed], complex fine tuning that puts one at a deeply isolated operating point in a configuration space, etc. These and the like are present in trillions of known cases and are reliable. In that context we have every right of valid scientific inference to conclude design in the world of life and cosmological origins, even as archaeologists infer to archaeology vs natural. And more, you have seen this many times but pretend it is not there, Fail. KF

  56. 56
    kairosfocus says:

    AF, strawman again. I pointed out how routinely we use measures of functional information on complex configuration in a digital world. The hyperskeptical, rhetorical pretence that FSCO/I is not routinely recognised and measured at first basic level itself speaks volumes about the self referential incoherence of objections like this. To object, you just created an instance of FSCO/I further exemplifying its known source, and you know it. This in the immediate context where you have yet to explain yourself on the pretence that it is not the general view of the informed that the cell has in it coded, string data structure, algorithmic information. KF

    PS, I remind you, on Lehninger’s matter of fact summary:

    “The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits . . . . A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function.” [Principles of Biochemistry, 8th Edn, 2021, pp 194 – 5. Now authored by Nelson, Cox et al, Lehninger having passed on in 1986. Attempts to rhetorically pretend on claimed superior knowledge of Biochemistry, that D/RNA does not contain coded information expressing algorithms using string data structures, collapse. We now have to address the implications of language, goal directed stepwise processes and underlying sophisticated polymer chemistry and molecular nanotech in the heart of cellular metabolism and replication.]

  57. 57
    kairosfocus says:

    JVL, the issue is how we get to lung fish as cell based life with a particular rather specialised body plan given the Lehninger point. Then we can debate theories as to how genome size can grow to seemingly anomalous size. KF

  58. 58
    JVL says:

    Kairosfocus: Further, there is the question, are there reliable signs of ART, yes: start with FSCO/I, include irreducible complexity under the Menuge factors C1 – 5, go on to active information that puts you on a shoreline of function.

    the issue is how we get to lung fish as cell based life with a particular rather specialised body plan given the Lehninger point. Then we can debate theories as to how genome size can grow to seemingly anomalous size.

    Sigh. Why you cannot answer two simple and direct questions is a mystery. So, I shall restate my questions again!

    What criteria do you use to detect the presence of FSCO/I? AND how do you determine the amount of FSCO/I present?

    Please just answer those two basic questions. Thank you.

  59. 59
    David P says:

    @Alan Fox at 45
    Bickering about analogies is simpler than discussing the main point of this article or my seemingly impaired attempt at understanding evolution. I’m willing to listen and learn though.

    “Successive rounds of variation and selection result in adaptive change.” Ok, got it.
    What about when successive rounds of variation and selection result in no adaptive change?
    I believe the word is stasis. What about that?

  60. 60
    kairosfocus says:

    JVL, stop pretending and use some common sense. If something depends for function on particulars of configuration, significant perturbation deranges function; which is observable. Why are there auto parts stores, why do we distinguish meaningful from garbled text and further from gibberish, why do we speak about debugging and how challenging it is, why are we so afraid of effects of radioactivity on our cells, etc? [Back in rad physics the primary mechanism we discussed was, damage to the commonest molecule H2O then damaging impact on key biopolymers by resulting highly reactive species. This issue directly shows how DNA is sensitive to perturbation.] As to how much/metrics you know full well this has been on the table since Orgel. That is, description or specification length in binary digits. There is adjustment on redundancy etc but a basic measure is obvious and commonplace. That is why I pointed to file sizes for computers i/l/o what I did to free up space a few days ago; surely ypou know such files are functional and distinct from garbled or corrupt files or ullage on a disk or the like. . You full well know this has been on the table for years, your hyperskeptical pretence that it is not there, has not been measured or is not measurable is gaslighting rhetorical nonsense. KF

    PS, for record, Orgel

    living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity . . . .

    [HT, Mung, fr. p. 190 & 196:]

    These vague idea can be made more precise by introducing the idea of information. Roughly speaking, the information content of a structure is the minimum number of instructions needed to specify the structure.

    [–> this is of course equivalent to the string of yes/no questions required to specify the relevant J S Wicken “wiring diagram” for the set of functional states, T, in the much larger space of possible clumped or scattered configurations, W, as Dembski would go on to define in NFL in 2002, also cf here,

    here and

    here

    — (with here on self-moved agents as designing causes).]

    One can see intuitively that many instructions are needed to specify a complex structure. [–> so if the q’s to be answered are Y/N, the chain length is an information measure that indicates complexity in bits . . . ] On the other hand a simple repeating structure can be specified in rather few instructions.  [–> do once and repeat over and over in a loop . . . ] Complex but random structures, by definition, need hardly be specified at all . . . . Paley was right to emphasize the need for special explanations of the existence of objects with high information content, for they cannot be formed in nonevolutionary, inorganic processes [–> Orgel had high hopes for what Chem evo and body-plan evo could do by way of info generation beyond the FSCO/I threshold, 500 – 1,000 bits.] [The Origins of Life (John Wiley, 1973), p. 189, p. 190, p. 196.]

  61. 61
    Caspian says:

    Seversky @20:
    Information, in the context of this discussion, is given a thorough definition with applications to biology and origin of life in Hubert Yockey’s book: Information Theory, Evolution, and the Origin of Life.
    https://www.amazon.com/Information-Theory-Evolution-Origin-Life/dp/0521169585.

  62. 62
    Alan Fox says:

    I believe the word is stasis. What about that?

    Well, it’s a point of view. I believe you are mistaken and that change is a fundamental property of this universe (which is changing, expanding at this moment). Continents are drifting, mountains are eroding, sea level rising.

  63. 63
    kairosfocus says:

    F/N: Note, WmAD: >>Essentially, specified complexity or specified improbability involves two notions of complexity, one probabilistic, the other linguistic or descriptive. Thus we can speak of probabilistic complexity and descriptive complexity. Events become probabilistically more complex as they become more improbable (this is consistent with, as pointed out earlier, longer, more improbable sequences of coin tosses requiring longer bit strings to be recorded). At the same time, descriptive complexity characterizes patterns that describe events via a descriptive language. Descriptive complexity differs from probabilistic complexity and denotes the shortest description that will describe an event. The specification in specified complexity thus refers to patterns with short descriptions, and specified complexity refers to events that have high probabilistic complexity but whose identifying patterns have low descriptive complexity. >> That is, in functionality context, complex organisation deeply isolated in the space of possible configs, but simply describable relative to function. A Book length string of say 10^6 ASCII characters — at 7 characters/word and 600 words/p. that’s about a 240 pp book — has 128^[10^6] possibilities, and it would be futile to try to generate by in effect flipping 10^6 coins over and over until a complex meaningful text in English emerges. That’s long before we get to a book that people would buy and recommend. But, writers routinely generate such. They do so based on knowledge, skill, intent and possibilities for creating codices. Nor is there a good path where we can flip 49 coins at a time then catch a word, go on to the next 49 coins and repeat to get a coherent book length message. Setting up 20,000 trays of 49 coins and incrementally selecting the best chain so far would likely fail too. Say, typical 40 characters per line of code and 1,000 lines, we have 40,000 characters in a program. We can test, compile and run to see if it executes. Debugging tells us there is a big gap between it runs and is bug free. This is a case where background enables us to put ourselves near an island of function and debugging at least puts us on a beach. But there is no incremental functioning at every step path from hello world to Linux. KF

  64. 64
    kairosfocus says:

    PS, see implications for when a self replicating facility is itself a huge increment in functionally specific organisation and information? See why active info from a knowledgeable designer is vastly more effective?

  65. 65
    David P says:

    Alan FOX @62
    I ask about successive rounds of variation and selection resulting in both adaptive change and no change and your reply is about continental drift, mountains, and sea levels?
    I’m willing to listen but obviously you don’t have the answers. This is a good example of why the tide is turning in the whole intelligent design debate.
    When someone asks a legit question- why there’s no change in some species while they are still surviving, varying, and passing that variation on to the next generation….and the answer is to simply ignore it.

    Ever heard of Giovanni Domenico Cassini? The guy refused to even look through a telescope for fear it might challenge his beliefs about light being instantaneous.

  66. 66
    kairosfocus says:

    DP,

    pardon my comments.

    The core theorems of neo-darwinism can be summarised:

    a: Incremental, chance variations [ICV] are caused by genetic variation aka mutation of various kinds [denial of Lamarckian thought]

    b: the environment poses a challenge so there is selection pressure where slight advantages lead to differential reproductive success DRS across ICVs, leading to descent with modification

    ICV + DRS –> DWM

    c: a wide variety of body plans are accessible (continent of functional forms, COFF) through DWM, so we have branching tree macro-evolution[BTME] thus descent with UNLIMITED MODIFICATION, [DWUM] and thence the tree of life [TOL]

    DWM + COFF –> BTME + DWUM –> TOL

    d: Stasis is the result of cases of robustly optimised organism populations [ROOP] at fitness functional peaks [FFP] which serve as point attractors giving genetic drift [GD] but stable body forms [SBF]

    TOL –> ROOP + FFP –> GD + SBF

    e: as the fitness landscape can vary gradually or catastrophically, we can have gradual loss of ROOP, or in some cases such as the 65 MYA impact, mass extinction and repopulation through fresh BTE, here, rise of mammals etc.

    Notice, the continent of continual forms implicit assumption. This is critical and lacks support, starting with protein fold domains, so the basis for fresh tissue types, organ systems etc is a challenge. More broadly, Orgel-Wicken functionally specific complex organisation and/or associated information [FSCO/I] requires many correct parts, correctly arranged and coupled to achieve function, so it naturally comes in islands widely separated by seas of non function. This includes that von Neumann/Drexler kinematic self replication is itself a huge increment in FSCO/I and is required for first cell based life. This issue was discussed in Paley Ch 2 of Nat Theol when he envisioned as a thought exercise a time keeping self replicating watch. He anticipated von Neumann by 150 years. This has been largely forgotten. So we have a vast configuration space for cells and body plans based on cells, but islands with viable cell types and body plans are deeply isolated in that space.

    To give an idea genome for first life would require 100 – 1,00+ kbases and body plans for multicellular organisms 10 – 100+ million. Bases are 4-state, two bits of info carrying capacity. The search resources of our sol system, 10^57 atoms or the observed cosmos 10^80, with 10^17 s and fast chem reaction rates of 10-14 s, could only sample a negligible fraction of the config space for 500 – 1,000 bits. This is the blind needle in haystack search challenge. Intelligence solves it by use of knowledge.

    Take the imagined continent and flood it with non functionality, what remains is isolated peaks.

    To get to origin of life and of body plans now becomes maximally implausible on blind chance and mechanical necessity, but is well within reach of design.

    Evolutionary adaptation can and does happen, but within islands of function. But it faces barriers to span the tree of life taxonomical framework at body plan level. Micro evolution is very different from macro.

    Hope this helps

    KF

  67. 67
    Alan Fox says:

    David P writes:

    I ask about successive rounds of variation and selection resulting in both adaptive change and no change and your reply is about continental drift, mountains, and sea levels?

    That was in response to your remark I believe the word is stasis. What about that? which is incorrect and I was just pointing out evidence that undermines your belief.

    I’m willing to listen but obviously you don’t have the answers.

    That is rather premature. Though I’m far from the best person to help you discover the wonders of evolutionary biology.

    This is a good example of why the tide is turning in the whole intelligent design debate.

    Just because another random commenter on an obscure blog can’t immediately convince you about evolution, you feel free to reject it? I think the rejection is deeper seated than that. As for “Intelligent Design”, when someone can tell me how it works rather than how evolution doesn’t, I’ll begin to take t seriously.

    When someone asks a legit question- why there’s no change in some species while they are still surviving, varying, and passing that variation on to the next generation….and the answer is to simply ignore it.

    I disagree with the premise of your question. Nothing is in stasis. The rate of evolutionary change depends on circumstances, and there is no reason to think the net rate of change is constant.

    Ever heard of Giovanni Domenico Cassini? The guy refused to even look through a telescope for fear it might challenge his beliefs about light being instantaneous.

    Indeed I have. I assume you mention it to indicate there is something I’m avoiding. What do you think that is?

  68. 68
    kairosfocus says:

    Do you want us to count the ways?

  69. 69
    Alan Fox says:

    Evolutionary adaptation can and does happen, but within islands of function.

    Excellent, KF. I think you are falling into another analogy trap, however. Niches can change. I assume you view the selection landscape as fixed. This is evidently not the case.

  70. 70
    kairosfocus says:

    AF, yet another rhetorical stunt. While I have followed others in using a metaphor, the underlying reality for Orgel-Wicken FSCO/I lies in Wicken’s “wiring diagram,” i.e. a specification as to ways components are arranged, oriented and coupled to achieve function. This inherently means there are vastly more ways for such parts to be clumped or scattered in non functional ways. A bait bucket of reel parts can be shaken around all you want, you will predictably fail to get a functioning ABU 6500 C3. A tray of 500 coins can be flipped at random all you want, you will not get ascii code for 72 letters worth of coherent English text. Similarly, D/RNA and AAs can follow each other in any sequence, an arbitrary string of 900 bases is maximally implausible as forming an algorithm to form a 300 AA protein chain that will fold and function properly. We could go on and on but the point about islands of function is clear, as is your determination to hyperskeptically dismiss anything that threatens your preferred narrative of origins. To that end you have posed on knowledge of biochem to dismiss the common consensus that D/RNA contains codes for protein synthesis. Only, to now be evading the likes of Lehninger’s intellectual heirs and Bruce Alberts. A sorry performance. KF

    PS, for varying fitness landscapes I already pointed to slow changes and catastrophies. The image I use is of barrier islands drifting and changing in the geography. That does not solve the prior function of establishing a beachead of function to enable incremental hill climbing. There is no good reason to believe in a continent of functional forms.

  71. 71
    Alan Fox says:

    AF, yet another rhetorical stunt.

    Nope, I just disagree with you on some issues.

    While I have followed others in using a metaphor, the underlying reality for Orgel-Wicken FSCO/I lies in Wicken’s “wiring diagram,” i.e. a specification as to ways components are arranged, oriented and coupled to achieve function.

    Nope. FSCO/I is yours alone. You have yet to demonstrate how it works.

    This inherently means there are vastly more ways for such parts to be clumped or scattered in non functional ways.

    Agreed. Dawkins, too. There are many more ways of being dead than alive.

    A bait bucket of reel parts can be shaken around all you want, you will predictably fail to get a functioning ABU 6500 C3. A tray of 500 coins can be flipped at random all you want, you will not get ascii code for 72 letters worth of coherent English text.

    m’kay

    Similarly…

    Uh-oh!

    …D/RNA and AAs can follow each other in any sequence, an arbitrary string of 900 bases is maximally implausible as forming an algorithm to form a 300 AA protein chain that will fold and function properly.

    This is the “one-needle-in-a-haystack” argument that fails on several points. It is well documented that a function can be supplied by more than one sequence, that function does not need to arise all at once (promiscuity to specificity), that there does not need to be an exhaustive search to find a function. Function does not equal sequence.

    We could go on and on but the point about islands of function is clear

    No. You are imprisoned by your own poor analogy. Fitness landscapes change.

    as is your determination to hyperskeptically dismiss anything that threatens your preferred narrative of origins.

    Oddly, I don’t feel threatened.

    To that end you have posed on knowledge of biochem to dismiss the common consensus that D/RNA contains codes for protein synthesis. Only, to now be evading the likes of Lehninger’s intellectual heirs and Bruce Alberts. A sorry performance. KF

    Happy for you to talk about codons, triplet codes, genetic code. The issue is not the names; it is how things work in reality.

  72. 72
    Alan Fox says:

    KF, no big deal, but do you have an aversion to paragraphs?

  73. 73
    kairosfocus says:

    AF, you can say what you want. It’s clear you have failed to reckon with Orgel and Wicken. It is further clear that your stunt of objecting to code has failed. You are left to double down. Fail. KF

  74. 74
    Alan Fox says:

    Declare yourself winner, KF, by all means.

  75. 75
    kairosfocus says:

    F/N: Just for record, Orgel:

    living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity . . . .

    [HT, Mung, fr. p. 190 & 196:]

    These vague idea can be made more precise by introducing the idea of information. Roughly speaking, the information content of a structure is the minimum number of instructions needed to specify the structure.

    [–> this is of course equivalent to the string of yes/no questions required to specify the relevant J S Wicken “wiring diagram” for the set of functional states, T, in the much larger space of possible clumped or scattered configurations, W, as Dembski would go on to define in NFL in 2002, also cf here,

    here and

    here

    — (with here on self-moved agents as designing causes).]

    One can see intuitively that many instructions are needed to specify a complex structure. [–> so if the q’s to be answered are Y/N, the chain length is an information measure that indicates complexity in bits . . . ] On the other hand a simple repeating structure can be specified in rather few instructions.  [–> do once and repeat over and over in a loop . . . ] Complex but random structures, by definition, need hardly be specified at all . . . . Paley was right to emphasize the need for special explanations of the existence of objects with high information content, for they cannot be formed in nonevolutionary, inorganic processes [–> Orgel had high hopes for what Chem evo and body-plan evo could do by way of info generation beyond the FSCO/I threshold, 500 – 1,000 bits.] [The Origins of Life (John Wiley, 1973), p. 189, p. 190, p. 196.]

    Then, Wicken on wiring diagrams

    ‘Organized’systems are to be carefully distinguished from ‘ordered’ systems. Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions and/or repetitive stepwise procedures] and therefore lack complexity, organized systems must be assembled element by element according to an [ –> originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65. (Emphases and notes added. Nb: “originally” is added to highlight that for self-replicating systems, the blue print can be built-in.)]

    The roots of my summary phrase are obvious, save to those threatened by the point.

  76. 76
    Seversky says:

    Talking about “information” and “complexity”, here is an apposite comment by Joe Felsenstein on The Panda’s Thumb

    (1) “complexity” in the Specified Complexity literature does not mean something like complicatedness. It just means improbability, under some null distribution. This is not a terminological mess due to creationists, but was a terminological mess originally made by Leslie Orgel, who is the originator of the notion of specified information.
    (2) Orgel did not in any way mean to imply that natural selection could not achieve a high level of specification (on some scale of goodness such as fitness).
    (3) William Dembski did mean that, though, and he justified this by saying that the probability was to be calculated based on “necessity” by which he meant to include all natural evolutionary mechanisms. Thus by definition it wasn’t specified complexity if natural evolutionary processes could achieve it.
    (4) So the argument goes: we can show that SC cannot be achieved by natural selection. How? Because by definition if it can be achieved by natural selection it isn’t to be called SC. So then how do we know there is SC? By showing (somehow, in ways mysterious) that this level of adaptation cannot be achieved by natural processes such as natural selection. So the whole argument over “specified complexity” achieves nothing you didn’t already know, and SC cannot be diagnosed in some simple straightforward way.

  77. 77
    jerry says:

    comment by Joe Felsenstein

    He was the focus of attention a couple weeks and it turned out to be irrelevant.

    Similarly here. Complexity is an easily understood idea. Felstein’s comment is essentially nonsense. It’s not clear what he is talking about. Specificity and complexness are completely different things.

  78. 78
    chuckdarwin says:

    Caspian/61
    From the Preface, p. X of Yockey’s book:

    I show in this book that only because the genetic message is segregated, linear, and digital can it be transmitted from the origin of life to all present organisms and will be transmitted to all future life. This establishes Darwin’s theory of evolution as firmly as any science. The same genetic code, the same DNA, the same amino acids, and the genetic message unite all organisms, independent of morphology. (emphasis added to second sentence)

    It’s pretty common knowledge that Yockey was a materialist and no friend of ID. But the point here is the forcefulness that he musters for the theory of evolution.

  79. 79
    Caspian says:

    CD @ 78:
    Here’s another quote from H. Yockey: “It is clear that the belief that a molecule of iso-1-cytochrome c or any other protein could appear by chance is based on faith.” (H. Yockey, “Information Theory and Molecular Biology”, Cambridge University Press, 1992).

  80. 80
    Seversky says:

    Isn’t that just another version of Hoyle’s Fallacy?

  81. 81
    kairosfocus says:

    AF, obviously, you need to be reminded of Lehninger, pretty much as weighty a reference on the topic as you get:

    “The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits . . . . A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function.” [Principles of Biochemistry, 8th Edn, 2021, pp 194 – 5. Now authored by Nelson, Cox et al, Lehninger having passed on in 1986. Attempts to rhetorically pretend on claimed superior knowledge of Biochemistry, that D/RNA does not contain coded information expressing algorithms using string data structures, collapse. We now have to address the implications of language, goal directed stepwise processes and underlying sophisticated polymer chemistry and molecular nanotech in the heart of cellular metabolism and replication.]

    This was only necessary to show that your gaslighting rhetorical gambit cuts across the otherwise non controversial consensus since the 50’s. Because you are aware of the devastating significance of finding coded algorithms in the heart of the cell, you have tried to rhetorically make it go away.

    Fail.

    Fail, that exposes your essentially irresponsible argumentation.

    KF

  82. 82
    chuckdarwin says:

    Seversky/80 re:
    Caspian/79

    Yup………
    There’s also the distinction that keeps getting glossed over on this blog, and, in more egregious cases, deliberately confused, between evolution and origins of life. The “appearance” of proteins falls in the latter category. I’m unaware of any biologist who claims the latter problem has been solved (other than the occasional ID proponent who has solved the problem via the grand designer AKA God).

  83. 83
    kairosfocus says:

    Sev, namecalling. We have a trillions member observational base that Orgel-Wicken type FSCO/I reliably comes about by intelligently directed configuration. Analysis of blind, needle in haystack search challenge in large configuration spaces readily shows why. Hoyle simply used a colourful metaphor. Specificity of organisation to achieve function is readily observed, as is the difference between high and low complexity, esp as WLOG we can discuss on strings. KF

  84. 84
    bill cole says:

    Isn’t that just another version of Hoyle’s Fallacy?

    It’s the reality of combinatorial mathematics. Hoyle so called “fallacy” is actually evolutionist denial. Hoyle understood mathematics most evolutionary biologists do not.

  85. 85
    Alan Fox says:

    There’s also the distinction that keeps getting glossed over on this blog, and, in more egregious cases, deliberately confused, between evolution and origins of life.

    Joe Felsenstein has a couple of acronyms for it, STOOL and OTOOL, “switch to or over to the origin of life”.

  86. 86
    Alan Fox says:

    Hoyle understood mathematics most evolutionary biologists do not.

    How did you make those assessments, Bill? Have you examples of biologists demonstrating that they do not understand mathematics?Mathematically speaking, most means more than half. Did you conduct a survey? Send them a test? What was your sample size?

  87. 87
    Alan Fox says:

    Analysis of blind, needle in haystack search challenge in large configuration spaces readily shows why.

    Nothing to do with evolutionary processes then.

  88. 88
    JVL says:

    Kairosfocus: FSCO/I reliably comes about by intelligently directed configuration.

    What is true: FSCO/I reliably comes about by intelligently directed HUMAN configuration.

    No other such agents have been detected or even defined. You want to assume them into existence but that’s not cricket.

  89. 89
    kairosfocus says:

    JVL, anthropomorphic fallacy and abuse of the logic of induction, repeatedly corrected. First, we all know that SETI has spent huge sums on the search for other intelligences, hoping for a valid wow signal. Well, there is one, just not coming from outer space, it is in the cells of our bodies. Then, for the record, as you know full well, we are contingent creatures and as such cannot exhaust the category: possible language using, knowing, technology developing, creative intelligences. What we demonstrate by example is that such entities are possible and what they can do. In that context if we find an object or state of affairs, X, with signs of intelligently directed configuration S, where we could not have been the source, then S is evidence for design by other intelligent agencies as cause of the evident design. Do you have good cause to infer that we are the only possible intelligences in the category? _______ My bet, no. Rhetorical gambit fails and inference to the best explanation applies. KF

  90. 90
    kairosfocus says:

    AF, Hoyle was a Nobel equivalent prize holding Astrophysicist and held deep knowledge of statistical thermodynamics, thus the logic behind the second law: overwhelming statistical weight of clusters of microstates. As a result of that he fully understood that blind needle in haystack search without operations on a Wicken wiring diagram design, was and remains maximally implausible as a credible account of the origin of configuration based function for entities far more sophisticated than a jumbo jet. Jumbo jets are full of FSCO/I, and mere injection of energy — tornadoes etc — does not adequately explain their organisation, even if the tornado hits a junkyard in Seattle. As for the molecular nanotech using cell, not only is its metabolism FSCO/I rich but it is from a known but not yet effected class of machine, a von Neumann kinematic self replicator automaton, here coupled to an encapsulated, smart gated metabolic entity and embedding a coded information record involving algorithmic instructions. Since Paley’s 2nd chapter we have/should have understood that this is a huge increment in Orgel-Wicken FSCO/I. That modern biological thought has often tried to argue that being an open, energy importing system is enough to escape this speaks volumes. As what needs to be imported is WORK — forced, specifically organised or ordered motion — according to a Wicken wiring diagram. KF

  91. 91
    JVL says:

    Kairosfocus: anthropomorphic fallacy and abuse of the logic of induction

    What I said is true: the only intelligent agents we have knowledge of that even come close to . . . what do you think the designer did? And when? . . . are human beings. You just assume there is some other being(s) out there, somewhere.

    What we demonstrate by example is that such entities are possible and what they can do.

    Possible but so far not observed or even detected.

    In that context if we find an object or state of affairs, X, with signs of intelligently directed configuration S, where we could not have been the source, then S is evidence for design by other intelligent agencies as cause of the evident design.

    But there is another explanation which requires fewer assumptions so is therefore more parsimonious. Your reasoning is motivated.

    Do you have good cause to infer that we are the only possible intelligences in the category?

    Your attempt to turn around my statement is noted. What I said is true: we have no knowledge or experience of any other intelligent beings in the universe. I happen to believe/hope there are some out there but there is zero evidence they exist and I admit that and do not attempt to shoe-horn them into any explanation I consider.

    If there are other intelligent beings in the universe the vast distances involved may mean we only ever communicate slowly via interstellar signals. We don’t live in a Star Trek or Star Wars universe. Let’s try and stick with what we know not what we wish. Don’t use unknown agents as explanations.

  92. 92
    kairosfocus says:

    JVL, the issue is the inference you hint at and invite by posing that as an objection not a mere observation. Which, you know. We are examining a case of known reliable signs of intelligently directed configuration in a context antecedent to and constituent of our existence and to that of cell based life on earth. That clearly points to intelligences of a similar class. As to traversal of distances, that is a secondary matter, we do not know what is possible regarding long range travel in our cosmos. What we do not know should not be used to block what we can readily know on reliable, observed sign. All of this you know. KF

  93. 93
    JVL says:

    Kairosfocus: We are examining a case of known reliable signs of intelligently directed configuration in a context antecedent to and constituent of our existence and to that of cell based life on earth. That clearly points to intelligences of a similar class.

    Not if there is a more parsimonious explanation that doesn’t require assumed agents and processes.

    As to traversal of distances, that is a secondary matter, we do not know what is possible regarding long range travel in our cosmos.

    To assume such travel is even possible is science fiction at this point. Again, science is about what we know not what might be true.

    What we do not know should not be used to block what we can readily know on reliable, observed sign.

    We should not make conclusions based on assumptions with no basis in evidence.

  94. 94
    kairosfocus says:

    JVL, there isn’t and you know it. Orgel-Wicken FSCO/I has been observed as caused trillions of times. It never comes from blind chance and mechanical necessity, for very good reasons as blind needle in haystack search challenge demonstrates. It is not a simpler, more reliable explanation you wish to impose it is an ideologically motivated lockout of the only category of cause known to be effective. Lewontin’s cat out of the bag moment haunts this matter. As to onward objections you set up and knock over strawmen. For example I simply pointed out that our ignorance on long distance travel cannot lock out far more direct observation of a reliable sign. As for using rejection of reliable sign to sugest and project to me unwarranted assumption, that is a first class violation of logic. As long as other intelligences of similar order are possible, signs count as evidence they were here. And you know it. KF

  95. 95
    Alan Fox says:

    The projection is strong with you, KF, arch knocker over of straw men. And you know it.

    Needle in haystack, one in a gazillion, all-at-once exhaustive searches… The list is long.

  96. 96
    kairosfocus says:

    AF, more rhetorical stunts, here, empty turnabout projection. Let us anchor to a specific point as for some time you have tried to make it seem an ill founded dubious notion that there is algorithmic code in the cell. Why did you claim or suggest such and what is your response to Lehninger et al backing up the commonly stated view, one that is taught down to primary school level. And that’s before we get to the direct import of start, elongate, halt elements in string data structures involving discrete state elements, here four not the two common in electronics. Of course there was that case of 3-state computers in the USSR that were quite promising and apparently cost effective. KF

    PS, just for convenient record, Lehninger:

    “The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits . . . . A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function.” [Principles of Biochemistry, 8th Edn, 2021, pp 194 – 5. Now authored by Nelson, Cox et al, Lehninger having passed on in 1986. Attempts to rhetorically pretend on claimed superior knowledge of Biochemistry, that D/RNA does not contain coded information expressing algorithms using string data structures, collapse. We now have to address the implications of language, goal directed stepwise processes and underlying sophisticated polymer chemistry and molecular nanotech in the heart of cellular metabolism and replication.]

    PPS, Similarly, kindly note the similar algorithmic pattern for creation of mRNA etc from DNA.

  97. 97
    Alan Fox says:

    Similarly, kindly note the similar algorithmic pattern for creation of mRNA etc from DNA.

    Nonsense. Between DNA strands, RNA strands, and DNA/RNA copying, there are hydrogen bonds designed (heh) in such a way so that adenine pairs with thymine and guanine pairs with cytosine/uracil. The result is duplication via a complementary strand. No algorithms necessary. This is basic stuff.

    The canonical genetic code only arises in protein synthesis, which is why RNA world is such a neatly plausible precursor.

  98. 98
    kairosfocus says:

    PPS, nope, not all at once exhaustive searches, just the well known blind needle in haystack challenge you full well know. It does not matter if you sample by all at once dust, random walk, blend of the two or by grand ensemble of cases, if search to space ratio is utterly negligible, you are unlikely to succeed. Where, remember, the first relevant search is in a Darwin pond or the like. Notice, my toy illustration, 10^57 atoms as observers updating at a fast rxn rate 10^-14 s, each with a tray of 500 coins [more realistically, paramagnetic domains, following good old Mandle in the Manchester Physics series or L K Nash], 10^17 s. Sol sys search model, 10^88 samples from a config space of 3.27*10^150 microstates. Less than 1 in 10^62. For cosmos scope, try 10^80 atoms and 1,000 coins each, far more swamped. Notice, just the genome of a first viable cell involves 100 – 1,000 k bases. For body plans, 10 – 100+ mn bases. Search challenge is real, just as real as the islands of function pattern naturally exhibited by FSCO/I. If you don’t like a 6500 reel as a simple toy case, compare the process-flow network of an oil refinery and that of cellular metabolism, which BTW has protein synthesis as a small corner. Recall, the cell has to integrate that with von Neumann/Drexler kinematic self replication.

  99. 99
    kairosfocus says:

    AF, there you go again, refusing to acknowledge what is laid before you, RNA polymerase constructs RNA on DNA step by step with initialisation and halting. That is on top of protein synthesis where the code use pattern is clear and is matter of fact in undeniably expert sources such as Lehninger. Not to mention many other readily accessible sources of lesser rank. You have some ‘splainin to do. KF

  100. 100
    Alan Fox says:

    I mean, this is so neat it bears repeating. The “beating heart”, the essential catalytic core of the ribosome is a ribozyme, a length of RNA. How is this coded for in the DNA sequence? It isn’t. The complementary copy is the ribozyme. Nothing has to be decoded or translated. It is just (I know) copied.

  101. 101
    kairosfocus says:

    JVL, had to pause to respond to AF. Please don’t overlook, that explanations have to cover all relevant factors. Including, that we are rational, responsible [so morally governed] creatures. The Haldane challenge is material in this context. KF

    PS, Haldane, for convenient record:

    [JBSH, REFACTORED AS SKELETAL, AUGMENTED PROPOSITIONS:]

    “It seems to me immensely unlikely that mind is a mere by-product of matter. For

    if

    [p:] my mental processes are determined wholly by the motions of atoms in my brain

    [–> taking in DNA, epigenetics and matters of computer organisation, programming and dynamic-stochastic processes; notice, “my brain,” i.e. self referential]
    ______________________________

    [ THEN]

    [q:] I have no reason to suppose that my beliefs are true.

    [–> indeed, blindly mechanical computation is not in itself a rational process, the only rationality is the canned rationality of the programmer, where survival-filtered lucky noise is not a credible programmer, note the functionally specific, highly complex organised information rich code and algorithms in D/RNA, i.e. language and goal directed stepwise process . . . an observationally validated adequate source for such is _____ ?]

    [Corollary 1:] They may be sound chemically, but that does not make them sound logically.

    And hence

    [Corollary 2:] I have no reason for supposing my brain to be composed of atoms. [–> grand, self-referential delusion, utterly absurd self-falsifying incoherence]

    [Implied, Corollary 3: Reason and rationality collapse in a grand delusion, including of course general, philosophical, logical, ontological and moral knowledge; reductio ad absurdum, a FAILED, and FALSE, intellectually futile and bankrupt, ruinously absurd system of thought.]

    In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter.” [“When I am dead,” in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209. Cf. here on (and esp here) on the self-refutation by self-falsifying self referential incoherence and on linked amorality.]

    That is a self-referential, material factor.

    PPS, of course, so is the demonstrable need for finitely remote necessary being as world root as traversal of an actually infinite, causal-temporal thermodynamic succession of years etc is an infeasible supertask. This intersects with the Haldane challenge.

  102. 102
    Alan Fox says:

    …of course, so is the demonstrable need for finitely remote necessary being as world root as traversal of an actually infinite, causal-temporal thermodynamic succession of years etc is an infeasible supertask. This intersects with the Haldane challenge.

    Everyone is entitled to their own religious view. What has this to do with biological sciences and protein synthesis?

  103. 103
    kairosfocus says:

    AF, there you go again ducking initiation, elongation step by step, halting. Those are the elements of algorithms FYI. And no explanation on the attempt to dismiss codes in protein synthesis. Oh most learned sage, given Lehninger’s status in biochem education for 50 years, explain why this text makes matter of fact reference to codes. KF

  104. 104
    Alan Fox says:

    RNA polymerase constructs RNA on DNA step by step with initialisation and halting.

    By directly templating and copying the sequence. There’s no code, just pairing of G/C or U and A/T.

  105. 105
    Alan Fox says:

    Though KF has triggered me into thinking how gene regulation works for mRNAs and I see I am a bit behind the curve on promoter sequences. Some reading is in order for me.

  106. 106
    Alan Fox says:

    KF

    AF, there you go again…

    You can read minds sometimes, KF. I’m away for a few days and won’t be troubling you much, if at all. Try and stick to the facts in my absence.

  107. 107
    kairosfocus says:

    AF, algorithms and code are not the same, algorithms can be built into hardware, e.g. cam bars. This is the issue of soft/hard partitioning. Algorithms are stepwise goal directed procedures with initialisation, execution steps, halting. That is what RNA polymerase is doing. And of course, for protein assembly we definitely have code use. Indeed, in recent years we have extended these codes or redirected into storing general purpose data. This has been repeatedly brought up here at UD, but obviously has been studiously ignored. Even as you continue to sidestep what Lehninger has had to say. All of this is adding up. KF

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