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ID Breakthrough — Syn61 marks a live case of intelligent design of a life form

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Let’s read the Nature abstract:


Nature (2019) Article | Published: 15 May 2019

Total synthesis of Escherichia coli with a recoded genome
Julius Fredens, Kaihang Wang, Daniel de la Torre, Louise F. H. Funke, Wesley E. Robertson, Yonka Christova, Tiongsun Chia, Wolfgang H. Schmied, Daniel L. Dunkelmann, Václav Beránek, Chayasith Uttamapinant, Andres Gonzalez Llamazares, Thomas S. Elliott & Jason W. Chin
Abstract
Nature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense codons and a stop codon in the genome. Thus, we recode 18,214 codons to create an organism with a 61-codon genome; this organism uses 59 codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA. [Cited, per fair use doctrine for academic, non commercial purposes.]

Let us refresh memory on the genetic code:

The Genetic code uses three-letter codons to specify the sequence of AA’s in proteins and specifying start/stop, and using six bits per AA

And on the DNA:

The DNA Helix with GCAT (HT: Research Gate, fair use)

Then also, protein synthesis:

Protein Synthesis (HT: Wiki Media)

Phys dot org gives some context:

A team of researchers at Cambridge University has replaced the genes of E. coli bacteria with genomes they synthesized in the lab. In their paper published in the journal Nature, the group describes replacing the genome and removing redundant genetic codes [–> three letter 4-state elements have 64 possibilities but only 20 are needed for typical protein AA’s, AUG codes for an AA and serves as START, there are three STOP codons] . . . . In this new effort, the researchers had two goals: The first was to synthesize the genome of an E. coli bacterium in their lab—all four million letters of it. The second was to find out what would happen to such a specimen if some of its DNA redundancies were removed . . . .

The researchers report that it took longer for the special bacterial specimen to grow, but other than that, it behaved just like unedited specimens. They suggest that in future efforts, it might be possible to replace the redundancies they removed with other sequences to create bacteria with special abilities, such as making new types of biopolymers not found in nature.

In short, they confirmed that the choice of “synonym” has a regulatory effect.

Where are we today, then?

First, we have definitive demonstration of the intelligent design of a genome. Yes, they obviously have not created a de novo cell body (a much more difficult task), but we see that intelligent design of life here definitively passes the Newton test of observed actual cause. Further, we see that DNA functions as an information system in the cell, supporting the significance of this conceptual representation, based on Yockey’s work:

I add: Let’s zoom in on Yockey’s contribution, on the code-communication system as applied to protein synthesis, which underscores the linguistic nature of what is involved:

Yockey’s analysis of protein synthesis as a code-based communication process

Where, Crick understood this from the beginning in 1953, witness p. 5 of his letter to his son Michael, March 19, 1953:

Crick’s letter

At this stage, we definitively know that using nanotech molecular biology and linked computational techniques it is feasible to construct a genome based on intelligently directed configuration. AKA, design.

Therefore, intelligent design, as of right not sufferance, sits at the table for study on origin of life and of body plans.

Where, we separately know on configuration space search challenge, that it is maximally implausible to construct in excess of 500 – 1,000 bits of functionally specific complex organisation and/or associated information. As a reminder:

We are now in a different ball game completely: Intelligent Design of life is demonstrated to be feasible and actual in the here and now, as of this investigation. Therefore, as of right, it is a serious candidate to explain what we see in the world of life; especially as regards origin of cell based life and origin of main body plans.

Going forward, we are now a full-fledged independent school of thought. END

PS: James Tour on the Mystery of Life’s Origin, challenging the usual OoL claims, focus from c. 8:30 on:

PPS: It seems we need to understand that there are such things as DNA Synthesisers. Here, is a sample, the “Dr Oligo”:

Biocyclopedia lays out the architecture:

Clipping the explanation:

Recently, fully automated commercial instrument called automated polynucleotide synthesizer or gene machine is available in market which synthesizes predetermined polynucleotide sequence. Therefore, the genes can be synthesized rapidly and in high amount. For example, a gene for tRNA can be synthesized within a few days through gene machine. It automatically synthesizes the short segments of single stranded DNA under the control of microprocessor. The working principle of a gene machine includes (i) development of insoluble silica based support in the form of beads which provides support for solid phase synthesis of DNA chain, and (ii) development of stable deoxyribonucleoside phosphoramidites as synthons which are stable to oxidation and hydrolysis, and ideal for DNA synthesis.

The mechanism of a gene machine is shown in Fig. 2.14 [–> above]. Four separate reservoirs containing nucleotides (A,T,C and G) are connected with a tube to a cylinder (synthesizer column) packed with small silica beads. These beads provide support for assembly of DNA molecules. Reservoirs for reagent and solvent are also attached. The whole procedure of adding or removing the chemicals from the reagent reservoir in time is controlled by microcomputer control system i.e. microprocessor . . . .

The desired sequence is entered on a key board and the microprocessor automatically opens the valve of nucleotide reservoir, and chemical and solvent reservoir. In the gene machine the nucleotides are added into a polynucleotide chain at the rate of two nucleotides per hour. By feeding the instructions of human insulin gene in gene machine, human insulin has been synthesized.

As in, molecular nanotech lab in action.

PPPS: As objectors have raised the claimed logical, inductive inference that designing intelligences are embodied (which we can safely hold, implicitly “lives” in the context of the presumed, evolutionary materialistic account of origins — of cosmos, matter, life, body plans, man, brains and minds), I first link a discussion of how this undermines rationality, by Craig:

I also put on the table the Smith, two-tier supervisory controller bio-cybernetic model, as a context to discuss embodiment, intelligence and computational substrates, first in simplified form:

The Derek Smith two-tier controller cybernetic model

Then, in more full detail:

This then leads to the gap between computation on a substrate and rational contemplation. That is, Reppert’s point holds:

. . . let us suppose that brain state A [–> notice, state of a wetware, electrochemically operated computational substrate], which is token identical to the thought that all men are mortal, and brain state B, which is token identical to the thought that Socrates is a man, together cause the belief [–> concious, perceptual state or disposition] that Socrates is mortal. It isn’t enough for rational inference that these events be those beliefs, it is also necessary that the causal transaction be in virtue of the content of those thoughts . . . [But] if naturalism is true, then the propositional content is irrelevant to the causal transaction that produces the conclusion, and [so] we do not have a case of rational inference. In rational inference, as Lewis puts it, one thought causes another thought not by being, but by being seen to be, the ground for it. But causal transactions in the brain occur in virtue of the brain’s being in a particular type of state that is relevant to physical causal transactions.

341 Replies to “ID Breakthrough — Syn61 marks a live case of intelligent design of a life form

  1. 1
    kairosfocus says:

    ID Breakthrough — Syn61 marks a live case of intelligent design of a life form

    It is time for a fresh conversation.

  2. 2
    kairosfocus says:

    F/N: particularly notice this from the abstract:

    ” we [–> the intelligent designers] recode [–> so much for the oh, DNA is not a code talking point] 18,214 codons [–> well beyond 500 – 1,000 bits of information] to create an organism with a 61-codon genome [–> 59 code for AA’s, AUG for Methionine also denoting start and three are STOP, where in other work that has been used for coding fresh AA’s]”

    Let us note, too, that the tRNA as folded has a standard CCA tool tip to which any AA could chemically couple, it is the loading enzyme that recognises specific conformation and attaches the proper AA. That is, we see where information and organisation come together in the system.

    18,000+ codons is so far beyond the 500 – 1,000 bit threshold for blind search implausibility on gamut of sol system to observed cosmos, that it is worth noting that also.

    We are in a different world as of this publication.

    This is a break in history of ideas, for me similar to my realisation at about 8:15 pm on the evening of July 18, 1995 — on hearing the Governor’s breaking the news of initial volcanic eruptions, that the future was going to be on a new line; confirmed early in October when the tip of that first cryptodome emerged.

    Or, like a fateful day in Nov 1963 or that morning on Sept 11 2001 for the world.

    Or even perhaps a day in AD 50 when the Areopagus’ members decided to entertain themselves intellectually by inviting a spermologos to speak to them, only to have their worldview upended with the Apostle Paul’s opening observations on a crucial point of ignorance. Sure, they literally laughed him out of court, and only a few responded positively. But to them belonged the future. Today, in Athens, the road by Mars Hill is named after the Apostle, then picks up with Dionysius the areopagite. Not only the verdict of history, but an apology and recognition of the man who carried forward the torch.

    Of course, this is a positive break-point, and one of global significance. Stay tuned for further developments.

    And yes, I am fully aware that likely those involved were not aware of the implications. Inadvertent admission is all the more powerful for that inadvertence.

    KF

  3. 3
    kairosfocus says:

    F/N2: It’s been coming for a few years now. Phys dot org also reports on earlier work at Harvard:

    August 19, 2016 report
    Researchers design and partially assemble a synthetic Escherichia coli genome

    by Bob Yirka , Phys.org

    An international team of researchers working in a lab at Harvard University has taken a bold step towards the development of a bacteria with a completely rewritten genome. They describe their work in a paper published in the journal Science and the reasons they believe the ultimate results will be safe for use in the real world. Science correspondent John Bohannon offers an In Depth piece on the work done by the team in the same issue and further discusses safety concerns tied to the new technology.

    Scientists would like to be able to modify the genomes of creatures because they believe such creatures could offer benefits to us humans that are not available naturally. One example would be changing the genome of a certain type of bacteria to make it immune to viral attacks—this would be important because we humans use bacteria in a variety of applications and viruses tend to cause problems in many of them.

    In this new effort, the researchers took a step into the future by eliminating redundant codons—triplets that represent four-letter DNA alphabet clusters—from the DNA of an E. coli bacterium, opening the door to the possibility of inserting new coding that would allow for the creation of new types of amino acids. To achieve this feat, they used machines to synthesize stretches of the genome (in its recoded form) and then inserted the chunks they had created into the genome of a living E. coli bacterium. The team managed to eliminate seven of the bacterium’s 64 natural codons in the chunks they inserted and were able to test approximately 63 percent of them. They report that doing so resulted in very few interruptions to natural functions, which suggests the technique may prove a viable means for creating an entirely new genome for a given creature. Perhaps more impressive is the possibility of creating new types of codons to replace the redundancies that were removed, which could, for example, endow bacteria or other creatures with new capabilities, such as producing amino acids that could fight off new types of viruses.

    The significance was already there, but of course nowadays we can count on burying of a very real but unwelcome headline.

    KF

  4. 4
    daveS says:

    KF,

    The significance was already there, but of course nowadays we can count on burying of a very real but unwelcome headline.

    An alternative take: People have been modifying the genomes of organisms for thousands of years (much more intentionally and precisely in recent years, no doubt). Every rancher’s herd of cattle is intelligently designed in that sense.

  5. 5
    daveS says:

    PS: I should say people have been “modifying genomes” at the population level for a long time using selective breeding. Not modifying the genome of a particular bull, for example.

  6. 6
    kairosfocus says:

    DS, this is NOT breeding, it is direct computer-aided synthesis of a complete genome using 61 instead of 64 codons. They recoded the genome, as they said. KF

    PS: Artificial selection is intelligent design, but it is not at the level we are dealing with here. I daresay, this is also a sign of one dimension of the coming Kondratiev long wave, along with AI and new energy technologies. Namely, molecular nanotech.

  7. 7
    MikeW says:

    As I understand it, the recoding of this bacteria’s genome is analogous to translating “The Art of War” by Sun Tzu from Chinese, where it uses about 5000 Mandarin symbols, to English, where it uses about 40 symbols. Why is this significant?

  8. 8
    daveS says:

    KF,

    DS, this is NOT breeding, it is direct computer-aided synthesis of a complete genome using 61 instead of 64 codons. They recoded the genome, as they said. KF

    Yes, the experiment clearly does not involve breeding, and is as you say. On the other hand, GMO’s have been around for some time.

  9. 9
    Brother Brian says:

    I would call this intelligent modification, not intelligent design. As DaveS has said, this has been going on for centuries. All that has changed is that we can now do this at the genetic level rather than affect the genome indirectly through selective breeding.

  10. 10
    kairosfocus says:

    MikeW, translation is immediately an act of intelligently directed configuration, i.e. design. Clearly the labs show ability to recode and synthesise, i.e. the technologies and mechanisms for a molecular nanotech lab relevant to engineering cell based life are demonstrated in successful action. We see that the means are empirically established and the fact of design of cell based life is demonstrated. We have passed the Newton Rules test. KF

    PS: Let me clip on Newton’s rules:

    Rule I [[–> adequacy and simplicity]

    We are to admit no more causes of natural things than such as are both true [[–> it is probably best to take this liberally as meaning “potentially and plausibly true”] and sufficient to explain their appearances.

    To this purpose the philosophers say that Nature does nothing in vain, and more is in vain when less will serve; for Nature is pleased with simplicity, and affects not the pomp of superfluous causes.

    Rule II [[–> uniformity of causes: “like forces cause like effects”]

    Therefore to the same natural effects we must, as far as possible, assign the same causes.

    As to respiration in a man and in a beast; the descent of stones in Europe and in America; the light of our culinary fire and of the sun; the reflection of light in the earth, and in the planets.

    Rule III [[–> confident universality]

    The qualities of bodies, which admit neither intensification nor remission of degrees, and which are found to belong to all bodies within the reach of our experiments, are to be esteemed the universal qualities of all bodies whatsoever.

    For since the qualities of bodies are only known to us by experiments, we are to hold for universal all such as universally agree with experiments; and such as are not liable to diminution can never be quite taken away. We are certainly not to relinquish the evidence of experiments for the sake of dreams and vain fictions of our own devising; nor are we to recede from the analogy of Nature, which is wont to be simple, and always consonant to [398/399] itself . . . .

    Rule IV [[–> provisionality and primacy of induction]

    In experimental philosophy we are to look upon propositions inferred by general induction from phenomena as accurately or very nearly true, notwithstanding any contrary hypotheses that may be imagined, till such time as other phenomena occur, by which they may either be made more accurate, or liable to exceptions.

    This rule we must follow, that the arguments of induction may not be evaded by [[speculative] hypotheses.

  11. 11
    kairosfocus says:

    DS, yes they have been around and were cited as first straws in the wind. This is a different level, the lab has done a full genome, synthesised and successfully put it to work. The technology is possible as it exists. The mechanisms of design have been demonstrated. Actual genome scale design has been effected. Of course, this is many miles away from full artificial synthesis of a cell, cf Tour’s remarks in the appended video lecture. Nevertheless a milestone. KF

  12. 12
    kairosfocus says:

    BB, have you ever heard, don’t reinvent the wheel? Instead, we modify, apply and adapt. That building on on an established technology is also design. Further, the context is that this demonstrates feasibility of mechanisms and technologies to do the job. Demonstrates, by actual doing. KF

  13. 13
    daveS says:

    KF,

    Not to understate the significance of this work, but the fact that it is now feasible is not exactly a bolt from the blue, is it?

  14. 14
    Brother Brian says:

    KF

    BB, have you ever heard, don’t reinvent the wheel?

    Sticking with that train of thought, if I change the tires on my car from Michelin to Good Year, and changed the thickness of the oil, am I really designing anything?

    From what I can discern from the abstract, they replicated the E.coli genome (all the same genes, in the same order) replacing codons with synonymous codons. Analogous to replacing all of a cars parts with after market parts made from different but equally effective metal alloy part.

  15. 15
    kairosfocus says:

    BB, I think you do not understand the molecular biology, chemical synthesis, computation etc involved in this. This is not changing a car tyre. I suggest you listen to the man who has done the chemistry, Tour. KF

  16. 16
    kairosfocus says:

    DS, yes, it was years and decades in the building. A milestone on a yet far longer journey to synthesise a full cell from scratch. But, sufficient to demonstrate the feasibility as a lab matter of design of cell based life forms. KF

  17. 17
    Brother Brian says:

    KF

    BB, I think you do not understand the molecular biology, chemical synthesis, computation etc involved in this.

    I understand it better than most, but definitely not at the level of the authors of the paper.

    We have had the technology to string together DNA in any arrangement we would like. It is, after all, just chemical reactions. What they did was to replicate an E. coli genome, gene by gene, identical to wild E. coli, with the exception that they replaced some “natural” codons with known synonyms for those amino acids.

    As far as I know (I only have access to the abstract) they did not create any new functionality. The analogy to replacing car parts is appropriate.

    If you want to use genetic engineering as “a breakthrough for ID”, I would recommend the numerous examples of introducing new functionality to plants that they didn’t previously have.

  18. 18
    turell says:

    Consider, if raw E. coli DNA, without the living cell body, is modified what is the result? We have modified raw DNA, but no living E. coli. So what is the point? Unless living organism are used, nothing is accomplished. Only existing life makes life. The citation of Tour is right on point. Proves nothing about the design of the origin of life.

  19. 19
    daveS says:

    KF,

    A milestone on a yet far longer journey to synthesise a full cell from scratch. But, sufficient to demonstrate the feasibility as a lab matter of design of cell based life forms.

    I’ll repost something I deleted earlier. It certainly will be interesting if scientists are eventually able to create designed organisms from scratch. But what if they end up creating a new conscious, intelligent lifeform?

  20. 20
    kairosfocus says:

    Turell, modification of the genome is important in itself as a scientific advance. The technologies allow us to tailor organisms to do things we need. Along the way, they managed to demonstrate the feasibility of intelligent design. Of course, as Tour discusses, creating a whole cell is a further very serious undertaking; but what was already done is a remarkable and significant achievement. KF

  21. 21
    MikeW says:

    Actually, now I think this recoding is more like starting with a book written in English, and recoding each “qu” with “kw”, and each “c” with “s” or “k”, thereby eliminating the need for the “q” and “c” keys on the keyboard. While this recoding might require some intelligence, I wouldn’t call it a “breakthrough”, and it says nothing about the intelligence required to write the original book.

  22. 22
    kairosfocus says:

    BB, the synthesis of a genome involving synonyms is itself a significant case of information-rich, intelligently directed configuration. The technological and knowledge base to achieve such already marks a major achievement, and demonstrates feasibility of intelligent design of life forms. We already have a significant case of design of a life form in hand. That has significant logical and epistemological import that fully justifies the headlined breakthrough. KF

  23. 23
    kairosfocus says:

    DS, the focal issue is, design of cell based life is demonstrated. That is a milestone. Its significance needs to be duly noted. Speculation on hoped for AI developments is tangential. KF

  24. 24
    kairosfocus says:

    MW, the breakthrough, first, is in the demonstrated technology to synthesise a genome under control of programmed instructions. The synthesis is itself a huge achievement, as Tour implies. (Have you watched his vid? This is a world class expert speaking.) Again, all that was needed for ID purposes was demonstration of intelligent design of life beyond 500 – 1,000 bits. This has been achieved with a whole genome with 18,000 genes. KF

  25. 25
    hazel says:

    Don’t go off on tangents, Dave! 🙂

  26. 26
    daveS says:

    hazel,

    Heh. 🙂

    I posted the same thing earlier and deleted it because I thought it too speculative, until I saw:

    I daresay, this is also a sign of one dimension of the coming Kondratiev long wave, along with AI and new energy technologies.

  27. 27
    ET says:

    That’s TWO cases of an intelligent agency producing a genome from scratch. And still ZERO for nature doing so.

    And until we learn how to program a living organism we won’t be able to synthesize a living organism.

  28. 28
    Fasteddious says:

    It would be interesting to put this modified E-coli into a normal batch to see how it competes, and whether there is horizontal gene transfer, and if so, how that affects the offspring. Would the new strain compete well or die out? Or would the new genes diffuse into the future mixed population? They mention that it took longer to grow. Why was that I wonder? Also, after N life cycles, would any of the missing 3 codons come back via random mutation? Lots of cool experiments they could do with this new batch…

  29. 29
    kairosfocus says:

    DS, in short the cluster of technologies points to huge possible economic implications of generational character. KF

  30. 30
    Brother Brian says:

    KF

    BB, the synthesis of a genome involving synonyms is itself a significant case of information-rich, intelligently directed configuration.

    But what was the original source of the information-rich configuration? It certainly wasn’t human. This human directed configuration didn’t provide any new information. It utilized existing information and substituted some synonyms. A not insignificant feat to be sure, but not exactly the ID breakthrough you claim it to be.

    But I am curious, were they able to use this new genome to create an organism from scratch, or did they utilize an existing cell and insert their replicated (with modification) genome?

  31. 31
    Brother Brian says:

    ET, welcome back. I think 🙂

  32. 32
    Mimus says:

    Lol. I have seen some weird claims on this site, but this might be the winner. When has the possibility that biomolecules could be intelligently tinkered with ever been questioned? The difference between this study and rational protein design or GM or CRISPR is only in the scale of the changes and the cool techniques used. I really can’t see how this realates to ID at all

  33. 33
    Mimus says:

    BB,

    Technologies like this are not yet able to make megabase molecules from scratch, so not only was the oraganism but entirety de novo (we are a long way from that!), Even the genome is a patchwork.

    Typically, you can swap out ~hundred kilobase regions of the target genome. So you start with the synthetic genome spread out across a bunch of bacteria, each with ~95% native DNA. You then use the cells own tricks to duplicate and recombine the pieces until you have a cell with only the synthetic genome.

  34. 34
    Brother Brian says:

    KF

    Turell, modification of the genome is important in itself as a scientific advance. The technologies allow us to tailor organisms to do things we need.

    But this isn’t exactly news. We have been using recombinant DNA and bacteria to produce insulin since the early 80s. But, again, we didn’t design insulin, we just used genetic engineering to get E. coli to produce it.

  35. 35
    Seversky says:

    It is not too much to say that every indication of Design in the Kosmos is so much evidence against the Omnipotence of the Designer. For what is meant by Design? Contrivance: the adaptation of means to an end. But the necessity for contrivance—the need of employing means—is a consequence of the limitation of power. Who would have recourse to means if to attain his end his mere word was sufficient? The very idea of means implies that the means have an efficacy which the direct action of the being who employs them has not. Otherwise they are not means, but an incumbrance. A man does not use machinery to move his arms. If he did, it could only be when paralysis had deprived him of the power of moving them by volition. But if the employment of contrivance is in itself a sign of limited power, how much more so is the careful and skilful choice of contrivances? Can any wisdom be shown in the selection of means, when the means have no efficacy but what is given them by the will of him who employs them, and when his will could have bestowed the same efficacy on any other means? Wisdom and contrivance are shown in overcoming difficulties, and there is no room for them in a Being for whom no difficulties exist. The evidences, therefore, of Natural Theology distinctly imply that the author of the Kosmos worked under limitations; that he was obliged to adapt himself to conditions independent of his will, and to attain his ends by such arrangements as those conditions admitted of.

    — John Stuart Mill, Three Essays on Religion

  36. 36
    Eugen says:

    I never read anything from John Stuart Mill. I always expected something smart from a person with a triple name but that maybe too much expectation

  37. 37
    hazel says:

    Very interesting quote, Sev.

  38. 38
    kairosfocus says:

    BB & Mimus:

    BB: But what was the original source of the information-rich configuration? It certainly wasn’t human. This human directed configuration didn’t provide any new information.

    M: Lol. I have seen some weird claims on this site, but this might be the winner. When has the possibility that biomolecules could be intelligently tinkered with ever been questioned?

    As a start, the issue is not (at this stage) any great originality in design — that will come (for good and ill . . . e.g. nextgen bioweapons) — but the simple fact that may be hard to focus: the actual, bare fact of demonstrated technical feasibility and actuality of genome scale . . . here, 18,000 genes worth . . . intelligently directed configuration of life forms as opposed to the much smaller scale changes we have seen for some years in genetic modification. Genome scale design is demonstrably feasible.

    We can also see a secondary demonstration: that as has been suggested for some time, synonyms affect rates of expression etc, thus have regulatory effect.

    Thirdly, as “recoding” strongly indicates, we are definitively dealing with a code, thus a language based information system, one that by its nature is antecedent to cell based life. That effectively sweeps off the table many objections over the years here at UD and elsewhere that no, the term code in genetic code is only a dismissible analogy. We are demonstrably dealing with codes that can be recoded, albeit with some effects that may be sub-optimal due to regulatory, likely context-sensitive effects of synonyms. This speaks to the known pattern of variants on a protein in similar life forms..

    Fourth, the codes are in the direct context of algorithms, there is framing of stored coded information, then AUG acts as START — add Met, there is elongation using the ribosome as assembly site, codon by codon in succession (that’s where substitutions occurred), there are finitely many steps leading to a STOP codon (three synonyms), then the AA chain is usually assisted in folding and we attain a clear goal, creation of a new protein molecule. Algorithms, using codes are strong indicators of intelligence, abstract thinking capability, purpose, a relevant knowledge base that allows programming how to move from a start point in steps to a desired goal, and linked machine technologies to achieve the practical implementation. Where in this case we are dealing with the difficult to work with molecular nanotech that Tour discusses in the video in the OP.

    Yes, strong evidence of language and technology using design antecedent not only to human designers (we are here riding piggyback on somebody else’s work) but to cell based life on earth. Of course, by itself, design of cell based life on earth does not demand more than a sufficiently sophisticated molecular nanotech lab. That’s a point ID thinkers have observed since the mid 1980’s, a point that keeps on being buried under by the flood of objecting rhetoric.

    (I will add, that when the evidence of design of C-chem, aqueous medium, code using cell based life is set in the context of a cosmos evidently fine tuned in ways that facilitate such, we get a very interesting broader picture. For example, the physics of our cosmos sets up as four most abundant elements: H, He, C, O; with N close enough. That’s stars, gateway to the periodic table, organic chem, water, amino acids. Add in a few others such as Si, Fe etc, and that’s terrestrial planets.)

    That cluster of findings is legitimately a breakthrough result, never mind predictable attempts by objectors to minimise its force. Of these, oh we all know that tinkering is possible and attempted lost in the dismissive laugh are clear fails.

    24 hours later, the point in the OP stands: this is a breakthrough that though inadvertent, definitively shows that genome scope design of life forms is a technically feasible proposition. Multiply that by codes being recoded (so, language) and by algorithms that were being modified (so, goal-directed action) and we find signatures of the known source of sophisticated design: language-using, purposive, knowledgeable, skillful intelligence.

    Thus we see code, language, algorithms, goals in action, here backed by demonstrated feasibility of relevant technologies. Design is therefore a serious candidate explanation for origin of cell based life and of major body plans. Ideologically driven exclusion following the materialistic a priori commitments Lewontin exposed long since, cannot be defended.

    KF

  39. 39
    kairosfocus says:

    Sev, citing Mill (& attn, H):

    It is not too much to say that every indication of Design in the Kosmos is so much evidence against the Omnipotence of the Designer. For what is meant by Design? Contrivance: the adaptation of means to an end. But the necessity for contrivance—the need of employing means—is a consequence of the limitation of power. Who would have recourse to means if to attain his end his mere word was sufficient?

    Such a clip is inherently tangential, but a reasonable short response that addresses the underlying error by Mill may help us understand the rationality involved in design.

    First, Mill’s bare assertions are little more than sour grapes rhetoric, turning on a gross strawman caricature of the theistic concepts of omnipotence and omniscience. A caricature comparable to imagining one has discredited the concept by asking whether God can build a square circle or make a rock so heavy and large it cannot be moved. These are pseudotasks, showing that words can frame things that are incoherent or impossible of being.

    Where, Mill seems to have overlooked the import of the Greek he learned from his father at ever so young an age: logos, the key theological and general term translated as Word (and which is explicitly set in the context of creation of “anything that was made”) implies communicative reason.

    Reason, which patently implies coherent adaptation of means to an end, here, an intelligibly ordered cosmos rather than a disjoint, incoherent, arbitrary, jumbled chaos. So, “contrivance” (an obvious allusion to Paley et al) is not arbitrary tinkering or incoherent arbitrariness, but intelligent, rational configuration to effectively attain an end, a purposed goal.

    On the first, kindly note a classic summary in the Catholic Encyclopedia:

    Omnipotence is the power of God to effect whatever is not intrinsically impossible. These last words of the definition do not imply any imperfection, since a power that extends to every possibility must be perfect. The universality of the object of the Divine power is not merely relative but absolute, so that the true nature of omnipotence is not clearly expressed by saying that God can do all things that are possible to Him; it requires the further statement that all things are possible to God. The intrinsically impossible is the self-contradictory, and its mutually exclusive elements could result only in nothingness. “Hence,” says Thomas (Summa I, Q. xxv, a. 3), “it is more exact to say that the intrinsically impossible is incapable of production, than to say that God cannot produce it.” To include the contradictory within the range of omnipotence, as does the Calvinist Vorstius, is to acknowledge the absurd as an object of the Divine intellect, and nothingness as an object of the Divine will and power. “God can do all things the accomplishment of which is a manifestation of power,” says Hugh of St. Victor, “and He is almighty because He cannot be powerless” (De sacram., I, ii, 22).

    As intrinsically impossible must be classed:

    Any action on the part of God which would be out of harmony with His [–> inherently good] nature and attributes;
    Any action that would simultaneously connote mutually repellent elements, e.g. a square circle [–> impossible of being], an infinite creature [–> such as the rock above], etc.

    A further point:

    The very idea of means implies that the means have an efficacy which the direct action of the being who employs them has not . . . if the employment of contrivance is in itself a sign of limited power, how much more so is the careful and skilful choice of contrivances?

    In this case, the omnipotent creator Mill targets, would be the creator of the cosmos, its laws and contents, so the means in question are his means, not entities he found lying around and managed to figure out how to turn to his goals. So, the mere LOGOS devises the means by calling them into existence, then working with them. Mill of course was 100+ years too early to know about fine tuning evidence.

    Going further, pure logic of being imposes all sorts of inherent limits on any possible distinct world, i.e. inherently. That is, arbitrariness is locked out. By this, I speak of what follows on some distinct possible world W as distinguished from a near neighbour W’ by some particular attribute A is on the table: W = {A|~A}. thus immediately, distinction, two-ness, simple unity, complex unity in the ~A, nullity in the partition, numbers following as {} –> 0, {0} –> 1, {0,1} –> 2 etc, with integers, rationals, reals, transfinites and complex numbers in train with innumerable constraints and relationships as well as possibilities, starting with, necessarily 2 + 3 = 5 etc. The rationality of being inherently entails highly specific properties, so the existence of constraints in a world is no proper objection to a being of the sort envisioned by theists.

    Accordingly, evidence of rational ordering of contingent aspects of the world should not be held as a counter argument in the way Mills tries.

    Coming back to main focus, this points to how intelligible rational ordering, specific functional organisation beyond a threshold of complexity that could plausibly be achieved by blind chance and/or mechanical necessity, codes, algorithms, language etc are signs of design. Designers configure means (material and conceptual) to ends. Indications of purpose, of knowledge, of skill, of creativity etc all point to not only the result design, but the credible source, a relevantly capable designer. Of course, this bare result does not necessarily specify any particular candidate.

    KF

  40. 40
    kairosfocus says:

    Turell, I should note, that DNA is part of the molecular complement of the living cell. We know that relevantly complex molecules can be synthesised chemically, and in the case of chromosomes, some of the biggest. We have focussed on this cell but the implications are much broader. What first needs to be empirically established (given a raft of objections and ideological lockouts) is that design is feasible and actual. Then, it cannot be properly excluded. Further to this, from Tour and general considerations on configuration spaces and implications of n bits implying 2^n possibilities, multiplied by 10^17 s or so and fast rxn rates being about 10^12 – 10^15/s, with 10^57 atoms in sol system and 10^80 in the observed cosmos, then blind needle in haystack search is not plausible as possible search scope is negligible relative to scale of config space. Where if one proposes a golden search, searches are samples so subsets, i.e. the space of possible searches for a space of 2^n possibilities is the power set, of space 2^[2^n], exponentially harder yet. When the requisite of correct, matched, clumped, properly arranged and coupled parts is added, we then see that config-based function comes naturally as deeply isolated islands in those large config spaces so hill climbing algorithms are defeated by the challenge to get to a shoreline of function (then to transition to the next island, cf OP illustration). Protein-relevant fold domains in AA sequence space is a clear molecular case in point. Design is demonstrated to be possible and it is a legitimate candidate cause. It is the strong horse causal explanation to beat. KF

  41. 41
    PeterA says:

    KF @6:

    Spot on
    Thanks

  42. 42
    kairosfocus says:

    Ever-watching (but silent) Invisible Remnant, see why I took time months ago to show that objections start with basic fact and logic, including necessary first principles and self-evident facts? When we move on to empirical observation and exercises, the pattern of hyperskepticism will continue. KF

  43. 43
    Mimus says:

    What are you smoking? Changing a bunch of “tag”s to “taa” proves the genetic code is “language”?

  44. 44
    kairosfocus says:

    PA, the molecular nanotech contribution to the next generation of economic growth? (FYI, Tour lists a cluster of emerging applications of molecular nanotech, including those relevant to life extension, breaking cancer, overcoming handicaps etc; potentially transforming demographics and productive lifespan. On AI, I note it is being used to try to tame the unruly plasma in the Tokamak fusion reactor, which if successful makes water the most important energy source in the world, one capable of taming deserts, providing H as energy carrier and of supporting sol system colonisation over the next couple of centuries.) KF

  45. 45
    kairosfocus says:

    Mimus,

    first, kindly address tone and resort to the ad hominem.

    By definition, design is intelligently directed configuration, here extended to manipulating the molecular nanotech of the genome, successfully, at full scale of 18,000 genes. Note what the researchers did:

    We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense codons and a stop codon in the genome. Thus, we recode 18,214 codons to create an organism with a 61-codon genome; this organism uses 59 codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA.

    Observe also the phys dot org report, again:

    In their paper published in the journal Nature, the group describes replacing the genome and removing redundant genetic codes [–> three letter 4-state elements have 64 possibilities but only 20 are needed for typical protein AA’s, AUG codes for an AA and serves as START, there are three STOP codons] . . . . In this new effort, the researchers had two goals: The first was to synthesize the genome of an E. coli bacterium in their lab—all four million letters of it. The second was to find out what would happen to such a specimen if some of its DNA redundancies were removed . . . . The researchers report that it took longer for the special bacterial specimen to grow, but other than that, it behaved just like unedited specimens. They suggest that in future efforts, it might be possible to replace the redundancies they removed with other sequences to create bacteria with special abilities, such as making new types of biopolymers not found in nature.

    They recoded and synthesised the full genome.

    Let me clip further from the report:

    The researchers report that they achieved both objectives by recoding the E. coli DNA on a computer with multiple redundancies removed. Once the desired genome was redesigned, it was split up and sent to a DNA synthesizer. The output from the DNA still needed tweaking, however, which meant the team had to stitch together smaller pieces into longer ones before it could be put into a living E. coli bacterium—they named it Syn61 because only 61 of the 64 possible codes were used.

    Also note the supplement in comment 3 on prior work at Harvard:

    researchers took a step into the future by eliminating redundant codons—triplets that represent four-letter DNA alphabet clusters—from the DNA of an E. coli bacterium, opening the door to the possibility of inserting new coding that would allow for the creation of new types of amino acids. To achieve this feat, they used machines to synthesize stretches of the genome (in its recoded form) and then inserted the chunks they had created into the genome of a living E. coli bacterium. The team managed to eliminate seven of the bacterium’s 64 natural codons in the chunks they inserted and were able to test approximately 63 percent of them. They report that doing so resulted in very few interruptions to natural functions, which suggests the technique may prove a viable means for creating an entirely new genome for a given creature [–> the current case is a milestone to that end]. Perhaps more impressive is the possibility of creating new types of codons to replace the redundancies that were removed, which could, for example, endow bacteria or other creatures with new capabilities

    That’s intelligently directed configuration, demonstrating the feasibility and efficacy of the technologies used as well as the soundness of the knowledge base applied.

    KF

    PS: The genetic code is just that, a code, a symbolic representation that joins two separate domains, a transmitting and a receiving. The key point is that the researchers spoke of “recoding” DNA and indeed that is exactly what they seem to have done. This highlights that it is acknowledged by relevant peer review in the leading scientific journal in the world, the one that happened to report the discovery of the double helix etc, that DNA is a molecule used to store and apply a code. Codes, are by their nature language. Language is a characteristic capability of relevant intelligence. If someone now argues that DNA is not code with implication of language, s/he is having a quarrel with Nature, not merely those despised “IDiots.”

  46. 46
    kairosfocus says:

    F/N: I suggest here on DNA Synthesisers, https://www.biolytic.com/t-dna-rna-oligo-synthesizer.aspx I am going to add a clip on that subject. KF

  47. 47
  48. 48
    daveS says:

    KF,

    Ever-watching (but silent) Invisible Remnant, see why I took time months ago to show that objections start with basic fact and logic, including necessary first principles and self-evident facts? When we move on to empirical observation and exercises, the pattern of hyperskepticism will continue.

    For my part, I simply believe that the hypothesis that the universe was intelligently designed is in the same place it was before the paper was published. This is an engineering breakthrough (I gather), but not a breakthrough in the science of origins.

  49. 49
    kairosfocus says:

    DS, the OP is not about the hyp that the observed cosmos was designed; that is tangential. It reports on the in the literature practical demonstration of intelligent design of a major component of cell based life, involving coded information and algorithms. Thus, the ideological exclusion of design as a serious consideration as a possible explanation of the cell, has no rational basis. And once design is allowed to sit to the table, it is immediately the strong horse. KF

    PS: As a FYI, the evident fine tuning that sets up our observed cosmos to a known deeply isolated operating point that enables C-Chem, aqueous medium, cell based life on terrestrial planets is in itself a serious candidate explanation for the observed cosmos, which does include such life.

  50. 50
    daveS says:

    KF,

    Thus, the ideological exclusion of design as a serious consideration as a possible explanation of the cell, has no rational basis.

    As far as I can tell no one excludes design because they think/thought the work in the paper was infeasible, rather pretty much everyone thought it was inevitable.

  51. 51
    Mimus says:

    Yes, they swapped out some codons for their synonyms. Do you think anyone who doesn’t accept ID is surprised that this is possible? It’s a great technical achievement, of course. But how does it change anything about our understanding of the genetic code, let alone prove this is a “language”?

    Do you really think anyone in the entire history of ID has objected to the idea based on the fact design of biological system was simply impossible? Even if there was such a person, how would swapping some codons for synonymous ones change their mind.

    What on earth are you reading in to this paper?

  52. 52
    kairosfocus says:

    F/N: I have expanded the info graph on telecomms, codes, and language. Particularly note Crick’s remarks in his own hand. KF

  53. 53
    kairosfocus says:

    Mimus, strawman. KF

  54. 54
    kairosfocus says:

    DS, the work directly demonstrates intelligent design on the genome, a key component of cell based life. The well known ideological exclusion is now even more clearly without rational basis. KF

  55. 55
    ET says:

    Brother Brian:

    But what was the original source of the information-rich configuration?

    It definitely wasn’t nature.

  56. 56
    ET says:

    JSM:

    For what is meant by Design? Contrivance…

    contrivance- the use of skill to bring something about or create something.

  57. 57
    ET says:

    daves:

    For my part, I simply believe that the hypothesis that the universe was intelligently designed is in the same place it was before the paper was published. This is an engineering breakthrough…

    So was the intelligent design of the universe, and the intelligent design of living organisms.

  58. 58
    PeterA says:

    KF @42:

    “objections start with basic fact and logic, including necessary first principles and self-evident facts”

    Yes.

  59. 59
    daveS says:

    KF,

    The well known ideological exclusion is now even more clearly without rational basis.

    Ideological exclusion tends to be difficult to justify rationally. 🙂

  60. 60
    Mimus says:

    Where’s the strawman? You have claimed this study as a breakthrough for ID. Surely for that to be true the results would need to include evidence that particular arguments put against ID were flawed. But nothing in this study does that. So where’s the breakthrough?

  61. 61
    Brother Brian says:

    KF

    DS, the work directly demonstrates intelligent design on the genome, a key component of cell based life.

    What exactly was designed? They replicated the genome replacing some codons with their known synonyms.

    I’m not saying that we will never be able to design an organism, or at least a unique genome with novel functionality that we can insert in a cell, but to call this paper an ID breakthrough is just not supported by the paper. Currently existing GMOs are much better examples of design.

  62. 62
    hazel says:

    mimus asks, “Where’s the strawman”.

    I’m not paying much attention to this thread, but I am interested in good discussion. The claim of “strawman” is often made without being specific. A strawman is an inaccurate description of another’s position, and then an argument against that inaccurate description.

    I think that when someone claims strawman, they should explain both what the accurate statement of one’s position is, and explain clearly how the other person has misrepresented it.

  63. 63
    kairosfocus says:

    DS, Notorious ideological exclusion:

    . . . to put a correct [–> Just who here presume to cornering the market on truth and so demand authority to impose?] view of the universe into people’s heads

    [==> as in, “we” the radically secularist elites have cornered the market on truth, warrant and knowledge, making “our” “consensus” the yardstick of truth . . . where of course “view” is patently short for WORLDVIEW . . . and linked cultural agenda . . . ]

    we must first get an incorrect view out [–> as in, if you disagree with “us” of the secularist elite you are wrong, irrational and so dangerous you must be stopped, even at the price of manipulative indoctrination of hoi polloi] . . . the problem is to get them [= hoi polloi] to reject irrational and supernatural explanations of the world [–> “explanations of the world” is yet another synonym for WORLDVIEWS; the despised “demon[ic]” “supernatural” being of course an index of animus towards ethical theism and particularly the Judaeo-Christian faith tradition], the demons that exist only in their imaginations,

    [ –> as in, to think in terms of ethical theism is to be delusional, justifying “our” elitist and establishment-controlling interventions of power to “fix” the widespread mental disease]

    and to accept a social and intellectual apparatus, Science, as the only begetter of truth

    [–> NB: this is a knowledge claim about knowledge and its possible sources, i.e. it is a claim in philosophy not science; it is thus self-refuting]

    . . . . To Sagan, as to all but a few other scientists [–> “we” are the dominant elites], it is self-evident

    [–> actually, science and its knowledge claims are plainly not immediately and necessarily true on pain of absurdity, to one who understands them; this is another logical error, begging the question , confused for real self-evidence; whereby a claim shows itself not just true but true on pain of patent absurdity if one tries to deny it . . . and in fact it is evolutionary materialism that is readily shown to be self-refuting]

    that the practices of science provide the surest method of putting us in contact with physical reality [–> = all of reality to the evolutionary materialist], and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test [–> i.e. an assertion that tellingly reveals a hostile mindset, not a warranted claim] . . . .

    It is not that the methods and institutions of science somehow compel us [= the evo-mat establishment] to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes [–> another major begging of the question . . . ] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute [–> i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door . . . [–> irreconcilable hostility to ethical theism, already caricatured as believing delusionally in imaginary demons]. [Lewontin, Billions and billions of Demons, NYRB Jan 1997,cf. here. And, if you imagine this is “quote-mined” I invite you to read the fuller annotated citation here.]

    KF

  64. 64
    daveS says:

    Ah, the riotously marked-up Lewontin article makes yet another appearance.

  65. 65
    ET says:

    Brother Brian:

    What exactly was designed?

    The genome was synthesized, meaning it is artificial.

    And guess what? No one has ever observed nature producing a genome.

  66. 66
    kairosfocus says:

    Mimus (& attn H),

    The strawman has already been documented, I now must wonder if I am seeing doubling down.

    Let’s start with, that design here speaks not so much to mere novelty or creativity or even artistry as to intelligently directed configuration, or contrivance.

    In the context of ID, we see:

    Design is an inherently iterative process requiring domain intelligence and expertise. Domain knowledge and experience can be applied to the procedure to decrease the time needed for a successful search. Because of the exponential explosion of possibilities (i.e. the curse of dimensionality), the time and resources required by blind search quickly become too large to apply.

    Undirected Darwinian evolution has neither the time nor computational resources to design anything of even moderate complexity. [–> hence the 500 – 1,000 bit threshold] External knowledge is needed. Neither quantum computing nor Moore’s law makes a significant dent in these requirements. [Marks, Dembski, Ewert, Introduction to Evolutionary Informatics, World Scientific, 2017, p.59.]

    If you glance at the PPS added to the OP you will see the relevant technologies behind the recoding and synthesis of over 4 million bases constituting a genome. Notice, what the Abstract that leads the OP reports:

    Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense codons and a stop codon in the genome. Thus, we recode 18,214 codons to create an organism with a 61-codon genome; this organism uses 59 codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA.

    You reduced this to the following simplistic and misleading characterisation, in 43 above:

    What are you smoking? Changing a bunch of “tag”s to “taa” proves the genetic code is “language”?

    We are dealing with a synthesis of a whole genome, effected in the molecular nanotech used in the cell. Synonyms as noted were substituted and the synthesised genome was used successfully in vivo. Further to this, the researchers “recoded” reflecting the recognition that the genetic code is precisely that, a code. As Crick recognised in 1953.

    FYI, this has been disputed by some hyperskeptical objectors; above, you come close. Do you recognise that a code is a linguistic phenomenon, inherently, and thus manifests language in action? Do you further recognise that protein synthesis on codes has a start, elongation in a finite stepwise process and halting, thus being algorithmic? Do you acknowledge that algorithms, by their nature are goal directed finite stepwise processes?

    We have here effective design and linked successful technologies demonstrated on a whole, recoded, synthesised genome. This is molecular nanotech at work successfully well beyond the 500 – 1,000 bit threshold, on the cell, Yes, as Tour highlights there is much more to go to synthesise a cell. That is onward but does not minimise the import of what has here been demonstrated.

    Namely — and regardless of naysaying and strawman rhetoric — demonstrated intelligently directed configuration of a synthetic genome that involves recoding, a genome that is further demonstrated to work.

    This is empirically demonstrated intelligent design in the relevant context.

    KF

  67. 67
    kairosfocus says:

    DS, strawman. You know full well that the ideological imposition thus documented, drawn out and highlighted has been on the ground for decades. KF

  68. 68
    hazel says:

    kf says, “The strawman has already been documented.”

    Be succinct and specific: what point has Mimus made that inaccurately describes your, or someone else’s, position?

  69. 69
    PeterA says:

    Their recoding apparently made a noticeable difference hence it affected something in the system.
    However, there could be other unnoticeable effects as well.
    For example, most Hispanics in Latin America have phonetically recoded the Spanish language by changing the way the letters C and Z sound. The Latin Americans make them both -specially the C- sound like S. Generally that doesn’t seem to affect the communication, but it can affect it because certain words become confusing when the C and Z are pronounced like S.
    For example, “ciento cincuenta” means “150” but spoken by a Latin American could mean to a Spaniard like “I feel 50” or “I sit 50” depending on the given context.
    Azufre (sulfur) said by a Latin American could mean to a Spaniard like “A suffers”, depending on the context.
    There are more examples.

  70. 70
    Mimus says:

    The “ecoding is not ‘further’ to the swapping in synonyms, as you seem to think, it’s just a term used to describe the swaps. I’m not sure how the fact that changing (yes, a lot of) codons to synonymous ones and still getting a functional genome is meant to be a breakthrough that changes the way we think of the genetic code.

    I also don’t think you are using strawman in the typical way.

    So, here’s a challenge: can you succinctly explain what claim my opponents of ID do these results undercut? If there are no such results, in what sense is this a breakthrough for ID?

  71. 71
    kairosfocus says:

    Mimus, I would be tempted to say doubling down, but I suspect you have not attended to what was done, synthesis of a genome using molecular nanotech, and usin machines likely to be similar to those described in the PPS. I also think you need to take time and read p. 5 of Crick’s March 19 1953 letter and let it soak in. KF

    PS: Any fool could look up a listing of the E Coli genome, and could pick some AA synonyms and substitute one stop code for another using the GCAT codes in text. That would already be a code exercise and a design effort, simple though that is; with the direct implication of language being at work. Not any fool could then take that, load it into DNA synthesisers, do edits and set ups then do the molecular scale operation to insert it in cells and make the cells operate on the synthesised genome, confirming that this is really so. It is the step 2 that is what makes it publication worthy and it is the implications of the technology that is being used to achieve this milestone which have the breakthrough significance.

  72. 72
    Brother Brian says:

    KF@71, nobody is denying that this is remarkable work. Where we disagree is your characterization of this as an ID breakthrough. Show me an example of someone using this technique to produce a completely novel gene resulting in a distinctly novel protein with a distinctly novel function and I would agree. Show me the use of this technique to create eyes using DNA strings, genes and proteins never seen before.

    I am not saying that this cannot be done, because I think that, eventually, it can be. The other point where we disagree is whether this is evidence for the intelligent design of life on earth. What it would be evidence for is that we have developed the ability to mimic biological life. For example, the fact that we can design and produce artificial diamonds, or artificial petroleum, does not provide any meaningful evidence that diamonds and petroleum are intelligently designed.

  73. 73
    Mimus says:

    Lol. I know why it as published, I asked you to defend the claim this paper is an “ID breakthrough”…

  74. 74
    hazel says:

    Even though I’m not paying attention to the details of the paper here, as I don’t have the background, I understand mimus’ point. People do intelligent things, and the issue of working with the genetic code certainly qualifies as intelligent work, but my understanding is that ID is about things happening through the means of some other intelligence of some sort. I agree with mimus that the one – intelligent design by people – doesn’t amount to a “breakthrough” for the hypothesis of intelligent design through non-human means.

    My layman’s 2 cents.

  75. 75
    kairosfocus says:

    BB (& attn Mimus), on track record and your likely provenance, objections, dismissals, side tracks and obsessive behaviour on your part are sadly predictable. I am not satisfied that you have seriously attended to what has been done and what it demonstrates, that using lab methods and equipment CURRENTLY in hand, researchers have synthesised a genome, inserted it in a cell and got it to work. FTR, even had they simply copied the genome of an E coli strain, that would be enough to show that intelligent design of key molecules and components of cell based life is feasible. Second, that they recoded and published in Nature directly implies that the professional guild of peers recognises that DNA is a coded molecule, which extends to mRNA directly. Whether or not you or your circle are inclined to admit it (on track record, a socio-psychological issue, not one of warrant), codes are linguistic phenomena, manifestations of language. Likewise, the protein synthesis code strings in DNA are algorithmic, manifesting start, stepwise incremental tasks and finitely remote halting, here also reflecting significant underlying domain knowledge. Algorithms are inherently purposeful, goal directed. Finally, the cumulative quantity of information is well beyond anything that blind forces could plausibly achieve on the gamut of the observed cosmos. Altogether it is now beyond reasonable dispute that intelligent design of such key systems is a viable option. Once the ideological lockout is removed, it is at once the strong horse. KF

  76. 76
    kairosfocus says:

    H, kindly note the just above. All that the objections game is doing in the face of the evidence on the table that is not being cogently addressed is confirming to anyone with doubts that we are not dealing with reasonable objections but determined ideological lockout. KF

    PS: Notice, what Mimus is failing to address, I will clip:

    Any fool could look up a listing of the E coli genome, and could pick some AA synonyms and substitute one stop code for another using the GCAT codes in text. That would already be a code exercise and a design effort, simple though that is; with the direct implication of language being at work. Not any fool could then take that, load it into DNA synthesisers, do edits and set ups then do the molecular scale operation to insert it in cells and make the cells operate on the synthesised genome, confirming that this is really so. It is the step 2 that is what makes it publication worthy and it is the implications of the technology that is being used to achieve this milestone which have the breakthrough significance.

  77. 77
    Mimus says:

    Well, after all this I’m still very much at “lol”. I know precisely what was done in this work, and agree it is a very impressive technical achievement. But it had precisely nothing to do with the plausibility of ID. You seem incapable of addressing any of the points put to you, or writing a clear and succinct message, so I guess I’m out.

  78. 78

    Of course, if you’ve managed to make yourself dead to the fact that when von Neumann predicted the organizational conditions of an autonomous self-replicator, he specifically predicted a multi-referent symbol system (and its necessary constraints, a la Turing and Peirce) as well as semantic closure at the very heart of the system (it was in fact, the whole point of the system), then no one should now expect you to care that our current manipulation of that system continues to confirm von Neumann’s already well-confirmed prediction. Your “lol”-ing at physical evidence should be rather expected.

  79. 79
    kairosfocus says:

    Mimus, more than enough has already been put on the table. KF

  80. 80
    kairosfocus says:

    UB, yes, unfortunately. I suspect there is lack of familiarity with machine language and communication systems, as well as the linguistic and symbolic import of codes. For sure the dismissive remark at 43 shows lack of awareness of the linguistic import of the 64 state code elements and their translation into AA space (noting the use of the universal CCA coupler on the tRNA). Here, compounded by failure to acknowledge that we have here genome scale synthesis with use of synonyms. This shows beyond reasonable doubt that a sufficiently sophisticated molecular nanotech lab can carry out effective genome scale designs. We do not yet have the full knowledge to feed into the techniques or to synthesise a cell from scratch, but that is a matter of time.

  81. 81
    Brother Brian says:

    KF

    Mimus, more than enough has already been put on the table. KF

    Translation: Comments Off. 🙂

  82. 82
    EricMH says:

    I agree with KF’s point here. While the researchers are not developing a novel genome, they have been able to recreate an organism from scratch. So, we have an instance of intelligent agency creating an organism. However, we’ve never observed Darwinian mechanisms creating an organism. All we have there is speculation. Thus, based on the rules for determining the cause for an effect that KF offers intelligent agency is the best causal explanation for the genetic code.

  83. 83
    Brother Brian says:

    KF@80, I don’t want to beat a dead horse, but didn’t all of the points of this comment exist (or so you believe) before this paper? What “groundbreaking” research did this bring to the ID myth?

  84. 84
    Brother Brian says:

    EricMH

    I agree with KF’s point here. While the researchers are not developing a novel genome, they have been able to recreate an organism from scratch.

    Have they? Were they able to take this replicated genome to create a new organism? How did they get the cell wall? The organelles? The whatever?

  85. 85
    hazel says:

    All kf’s arguments about DNA being a code, hence ID, are old and have been on the table for a long time. They may be valid, or they may not, but I don’t think the work done in this paper changes anything about the validity of those arguments. I think that is the point mimus is making.

  86. 86
    Brother Brian says:

    Hazel

    I think that is the point mimus is making.

    That is the point we are all making. It is excellent genetic research. It is excellent genetic engineering research. It definitely is not groundbreaking ID research. I don’t recall Axe, Gauger, Gunter, Behe, Klinghoffer, KF, ET, etc. being coauthors on this paper. This was authored by people who accept natural evolution. KF and others are free to submit their own papers to Nature or any other peer reviewed journal. But they won’t.

  87. 87
    PeterA says:

    Is this the first time that synthesis of Escherichia coli with a recoded genome has been achieved?
    Yes? Then Breakthrough.

    Was the procedure designed by intelligent agents?
    Yes? Then ID breakthrough.

  88. 88
    hazel says:

    Peter, does this mean that every time human beings create something significantly new and creative, such as some new technology, software, medical process or medicine, etc., we’ve had an ID breakthrough?

  89. 89

    the ID myth

    The only myth on display here is the myth that the promoters of an unguided origin of the organization enabling biology have a remotely coherent model of its unguided origin. They don’t. You don’t. Most won’t even talk about it. There is also the myth, of course, that the history and products of science supports their claims. It doesn’t,

    arguments about DNA being a code, hence ID, are old and have been on the table for a long time.

    This line is a positioning statement against physical evidence; it’s permission to continue ignoring it. Nothing else should be expected.

  90. 90
    kairosfocus says:

    H, I see:

    kf’s arguments about DNA being a code

    First, kindly scroll up to the OP and take time to read p. 5 of Sir Francis Crick’s March 19, 1953 letter to his son explaining his discovery; yes, it is in his own handwriting and he underlined the is in “the D.N.A. is a code.” You have tried to play the personalise-polarise tactic only to find the person you are arguing with is Crick. That should tell you something.

    Next, kindly observe what Yockey had to say, and the framework he used, which comes from Shannon et al. This is essentially a standard communication system framework applied to the protein synthesis system and process. Which, is pivotal to cell based life.

    Third, in my own right, I can indeed recognise codes, communication systems and algorithms in action, which is what we are seeing. Indeed, any competent person can; it is that obvious. That’s why — as was noted — the researchers spoke of RE-coding the genome to substitute synonyms where there is redundancy.

    So, yes, the prediction is about 70 years old and the confirmation played out across the next decade or two. That’s an old argument, but a sound one. Just, it is obviously not a conclusion that determined objectors to the design inference want to admit as credible. But in so acting, they only show that the case is actually strong.

    KF

    PS: In this context, lab based molecular nanotech directly relevant to synthesis of a living cell, the breakthrough of a genome is evidence of the feasibility of intelligent design of the cell using lab techniques. A point, that is patent. The attempts to deny, dismiss and deflect simply inadvertently underscore its force.

  91. 91
    EricMH says:

    @BB from the abstract looks like they recreated the genome from scratch.
    Anyways, your disagreement with KF is due to the researchers not creating a new genome, they are copying and refactoring an existing genome. That’s more than I’ve ever seen natural selection and random mutation ever do. And since whatever generated the genome in the first place has to be able to do what these researchers did, then the study shows intelligent agency at least on par with the researchers is necessary to create a genome. Thus, KF’s argument still stands.

  92. 92
    PeterA says:

    “The success of this project shows for the first time that living organisms can be created with compressed genetic codes.“

    “this study is the first time any commonly used model organism has had its genome designed and fully synthesised and this synthetic version could become an important resource for future development of new types of molecules. “

    “This monumental paper, which Jason’s group have been aiming towards for several years, was achievable through the hard work of many members of the group, as well as assistance from the LMB’s Mass Spectrometry and Light Microscopy facilities.”

    https://www2.mrc-lmb.cam.ac.uk/creating-an-entire-bacterial-genome-with-a-compressed-genetic-code/

  93. 93
    PeterA says:

    EricMH @91:

    Spot on.

  94. 94
    PeterA says:

    Hazel @88:

    Yes, of course! 🙂

    Definition of breakthrough
    1 warfare : an offensive military assault that penetrates and carries beyond a defensive line
    2 : an act or instance of moving through or beyond an obstacle
    a breakthrough in the talks between the region’s leaders
    a breakthrough agreement
    3a : a sudden advance especially in knowledge or technique
    a medical breakthrough
    b : a person’s first notable success
    a breakthrough novel
    the actress’s breakthrough performance

  95. 95
    kairosfocus says:

    PA:

    Is this the first time that synthesis of Escherichia coli with a recoded genome has been achieved?
    Yes? Then Breakthrough.

    Was the procedure designed by intelligent agents?
    Yes? Then ID breakthrough.

    Yes.

    KF

    PS: And, a key line of resistance having been broken, attempts are being made to seal off to prevent breakout. Hence, the statement of independence.

  96. 96
    daveS says:

    I guess that answers hazel’s question in the positive.

  97. 97
    hazel says:

    kf, you write, “You have tried to play the personalise-polarise tactic.”

    I don’t think resorting to ad hominems about tactics is very useful. I know enough about genetics to know that there is code, which you posted a chart of in your OP. I already said that “They may be valid, or they may not,” by which I meant arguments that life, and the genetic code, have been designed, as ID posits, may or may not be true.

    I’m not invested in that argument, and I am not arguing one way or another for it. But arguing for or against that is not the point of the discussion. The point of the discussion is that the recent work done as discussed in the paper is about the intelligent work human beings can do with what has already been created. It doesn’t add anything new to the arguments that life has been designed.

    I think PeterA succinctly shows the flaw in discrepancy between what your headline states and your further arguments about design. PeterA wrote,

    Is this the first time that synthesis of Escherichia coli with a recoded genome has been achieved?
    Yes? Then Breakthrough.

    Was the procedure designed by intelligent agents?
    Yes? Then ID breakthrough.

    This is, I think an empty and useless argument, in that it implicitly claims that any breakthrough by humans, acting as intelligent beings, is also a breakthrough for the larger ID argument that life was designed. The second doesn’t follow from the first.

    So I suggest you address this distinction instead of personalising and polarising the discussion.

  98. 98
    Brother Brian says:

    EricMH

    Anyways, your disagreement with KF is due to the researchers not creating a new genome, they are copying and refactoring an existing genome.

    No. My disagreement with KF is that he selects this as an ID breakthrough, even though it resulted in zero (nada, zip, bupkis) in the way of new functionality. Yet, he has completely ignored countless examples of genetic engineering that has demonstrated significant changes in genomes and subsequent functionality.

  99. 99
    ET says:

    Brother Brian:

    This was authored by people who accept natural evolution.

    The same authors who cannot demonstrate that nature can produce genomes? The same authors who cannot tells us how to test the claims of blind watchmaker evolution? The same authors who cannot find a scientific theory of (natural) evolution?

  100. 100
    ET says:

    hazel:

    Peter, does this mean that every time human beings create something significantly new and creative, such as some new technology, software, medical process or medicine, etc., we’ve had an ID breakthrough?

    Materialism definitely didn’t play a role. Blind watchmaker evolution definitely didn’t have a role.

  101. 101
    Brother Brian says:

    ET, did anyone mention how much you were missed over the last week? Not even KF? I didn’t think so.

  102. 102
    PeterA says:

    Hazel @97:

    You’ve got it wrong, buddy.

    Try again.

    ID is empirically based on the undeniable fact that the complex functionality and functional complexity we see around us are the product solely of the creativity of conscious agents.

    The title of this OP is correct. The whole OP is valid.

  103. 103
    PeterA says:

    Brother Brian @101:

    Can you explain what you tried to say in your comment? Is it related to this discussion?

    Thanks

  104. 104
    ET says:

    Well, Brother Brian, if it is of any consolation, I definitely didn’t miss reading your mindless drivel.

  105. 105
    Brother Brian says:

    PeterA

    Brother Brian @101:

    Can you explain what you tried to say in your comment?

    I can. But I choose not to.

  106. 106
    Mimus says:

    Anyways, your disagreement with KF is due to the researchers not creating a new genome, they are copying and refactoring an existing genome. That’s more than I’ve ever seen natural selection and random mutation ever do.

    I sometimes wonder if this place is for real, or if there personas are just an elaborate joke…

  107. 107

    arguments about DNA being a code

    I know enough about genetics to know that there is code

    Well, is there a code or not? What kind of code is it?

    Is it a multi-referent code? Does it use the spatial orientation of a set of objects in a common medium in order to distinguish and specify one referent from another? Is it a context specific code? Does it require a set of constraints in order to establish what it specifies? Must it describe those constraints? Does it also describe the organization of a dissipative process, one that causes the medium to be successfully actualized by the constraints? Does it’s success require a simultaneous functional relation between a) the descriptions of the constraints, and b) the descriptions of the dissipative process? Are there any other examples of such a system known to the physical sciences?

  108. 108
    hazel says:

    re 107. I don’t know nearly enough to know specifically what all those questions mean, but I don’t think there is anything else like DNA, genes, and all the associated apparatus that is part of living things. Not sure why you asked me all that, though.

  109. 109

    .
    So you know enough about the gene system to know it uses a code, but you don’t know if that code specifies multiple referents?

    Oh Okay.

  110. 110
    kairosfocus says:

    H, I refer you again to the OP, starting with Crick’s letter; cf, 90 above. It is you who personalised and dismissed an argument tracing to a Nobel prize winner and on the prize winning work, to me the better to dismiss as “old.” On being instructed in 90 to consult Crick, you instead have in 97 projected to me using what can on fair comment be termed the “he hit back first” argument. Please, instead address what Sir Francis pointed out March 19, 1953. At this point, you will know why for cause the dismissive objection you implied, fails. Where, the DNA code (as is tabulated) uses three-letter codons of four states per letter, to stipulate 20 AA’s used in the cell (apart from a few oddball cases), in about two dozen variant forms. These are set in a string data structure, and among other functions, specify algorithms to build proteins (see OP diag on protein synthesis), start + add Met, extend, extend . . . stop, the AA string being folded and modified to function, perhaps with other components. Other information is present for regulation, assembling RNA’s, etc. Sometimes there is discussion of multiple, interwoven codes. KF

    PS: BTW, the specific research demonstrated how genome scale synthesis can be carried out using lab equipment now available, and how the result works in a living cell, which is effectively a new, synthetic strain of E Coli, being named Syn61 for obvious reasons. This is directly relevant to intelligently directed configuration of genomes in the lab, thus demonstrating technical feasibility of lab based design of entire genomes. Such speaks to OoL and origin of body plans i/l/o demonstrated intelligent design in action. So the attempt in 97 to suggest an irrelevant argument fails. Fails in a way that inadvertently shows the strength of the point in the OP.

  111. 111
    Mimus says:

    This is directly relevant to intelligently directed configuration of genomes in the lab, thus demonstrating technical feasibility of lab based design of entire genomes

    Ok, I’ll try one more time…
    Has any ID skeptic ever argued that ID was flawed because “designing” genomes was technically difficult? That a genome could coveciably be designed has never been an issue. The fact that one has (or at least more bases have been altered than was previously possible…) is therefore neither here nor there when it comes to assessing the plausibility of ID. So, this research may well be a breakthrough but it’s hardly an ID breakthrough.

  112. 112

    .
    #111
    The genome is a symbol system, just as it was predicted to be. Every scheme imaginable (to avoid and denigrate that fact) has been applied against ID, including yours.

  113. 113
    kairosfocus says:

    Mimus,

    perhaps you are unaware of it but the possibility of intelligent design of cell based life and of body plans has been ideologically locked out and heavily slandered for many years by strident advocates of various stripes.

    The direct, peer review published demonstration of genome scale design and effecting of same (never mind no great novelty) directly answers that lockout and those smears. If such designs are effected here and now with our early days technology, what could an advanced molecular nanotech lab do? (I think within a century, we will be capable of synthesising a living cell from scratch, noting the challenges Tour highlights, cf. PS to OP.)

    Let me add: This exercise demonstrates that intelligent design at genome scale for cell based life is a fact. If it is a fact in the here and now, it must be allowed a place as a possibility at the point of origin of life on earth, and at origin of body plans. Or else, we are seeing the distortion of science on origins through ideological lockout. Censorship, in short. And if science on origins is being ideologically warped from its proper goal of unfettered exploration of the truth about our world, then that too is vitally important for us to know: science that has become atheistic ideology in a lab coat . . . see Lewontin . . . is self-discredited.

    Which carries the implication that resistance to acknowledging what the results in view put on the table is itself telling a story.

    It also puts on the table what ID proponents have publicly stated since the 1980’s. The biological evidence of design does not by itself require an inference as to whether relevant designers are within or beyond our cosmos. That is, the design inference on tested reliable signs such as FSCO/I or irreducible complexity etc, is an inference to process of design not to identification or ontological categorisation of candidate designers.

    Evidence of the fine tuned cosmos is another matter as that points to a cosmos-building designer who would necessarily be beyond our cosmos.

    What this development demonstrates is the feasibility of genome scale design of life forms using lab equipment in labs; we have been routinely accused of inferring from alleged evidence to God as supernatural designer, in order to try to characterise ID as anti-scientific, as a theological exercise dressed up in a lab coat.

    Ironically, the point that the OP implies — we cannot directly infer to God or the like as designer of the world of life on evidence of design of life forms — which has been readily accepted by ID thinkers since the mid 1980’s, is being lost in what looks rather like an attempt to rhetorically seal off a breakthrough.

    KF

  114. 114
    PeterA says:

    Mimus @111:

    Did you mean:
    conceivably
    convincible
    ???

    Thanks

    🙂

  115. 115
    PeterA says:

    Brother Brian @105:

    Your choice clearly shows your real motives in this discussion. Thanks for confirming it.

  116. 116
    kairosfocus says:

    UB,

    unfortunately, you are correct.

    It is sad that with Crick’s letter on the table as at March 19, 1953, objectors are unable to acknowledge the force of the evidence that DNA is machine stored code, which is transcribed with a substitution T –> U in mRNA then translated during algorithmic protein synthesis.

    The root of that translation is that tRNA’s (which have a common CCA tool tip that chemically could link any AA) are loaded through loading enzymes that sense their conformation. These then start or elongate protein chains in ribosomes, through the correspondence of codons and anti-codons. Where, the anticodons are on the opposite end of the loaded tRNA from the attached AA.

    So, this is translation, as is shown in the RNA form genetic code in the OP, moving from 64 codon (so anticodon) possibilities to 20 AA’s in the standard dialect, there being about 2 dozen dialects. Where, too, AUG serves as a start codon and there are three stop codons, showing key features of algorithms, initiation, stepwise process, finitude and halting.

    The associated communication system is also illustrated, e.g. by Yockey, in which peer layers interact with encoding and decoding, noting T in DNA –> U in mRNA. So BTW, the research also parallels a step in life, transfer to a synonym.

    Codes are inherently linguistic phenomena, which are a characteristic feature of intelligence.

    Which is the obvious sticking point: the evident, acknowledged manifestation of language has to be rejected to maintain the dominant school of thought.

    KF

  117. 117
    PeterA says:

    Mimus @106:

    Ty umnitsa, prosto molodyets!

    🙂

  118. 118
    kairosfocus says:

    H, kindly read p. 5 of the Crick letter in the OP and explain to us why Crick stated therein — in his own handwriting with an underscore on the is — that “the D.N.A. is a code,” then why you take the view you seem to. KF

  119. 119
    PeterA says:

    From Wikipedia, which is light-years from becoming an ID-friendly venue:

    The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA or mRNA sequences) into proteins. Translation is accomplished by the ribosome, which links amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.[1]

    The code defines how sequences of nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions,[2] a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme (see the RNA codon table). That scheme is often referred to as the canonical or standard genetic code, or simply the genetic code, though variant codes (such as in human mitochondria) exist.

    While the “genetic code” determines a protein’s amino acid sequence, other genomic regions determine when and where these proteins are produced according to various “gene regulatory codes”.

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

    PS. Sorry for repeating something that has been posted here gazillion times. But maybe the penny will eventually drop for some folks here?

    🙂

  120. 120
    OLV says:

    KF,

    Excellent OP and follow up commentaries. Thanks.

    UB,

    Check this out:

    Choreography of molecular movements during ribosome progression along mRNA
    Riccardo Belardinelli, Heena Sharma[…]Marina V Rodnina
    Nature Structural & Molecular Biology volume 23, pages 342–348 (2016)

    How Messenger RNA and Nascent Chain Sequences Regulate Translation Elongation
    Article (PDF Available)?in?Annual Review of Biochemistry 87(1):421-449

    BTW, missing GP very much.

  121. 121
    kairosfocus says:

    OLV,

    Yes, he must be busy elsewhere likely RW.

    I clip the Abstract:

    https://www.nature.com/articles/nsmb.3193

    Article | Published: 21 March 2016
    Choreography of molecular movements during ribosome progression along mRNA

    Riccardo Belardinelli, Heena Sharma, Neva Caliskan, Carlos E Cunha, Frank Peske, Wolfgang Wintermeyer & Marina V Rodnina

    Nature Structural & Molecular Biology volume 23, pages 342–348 (2016) | Download Citation
    Abstract

    During translation elongation, ribosome translocation along an mRNA entails rotations of the ribosomal subunits, swiveling motions of the small subunit (SSU) head and stepwise movements of the tRNAs together with the mRNA. Here, we reconstructed the choreography of the collective motions of the Escherichia coli ribosome during translocation promoted by elongation factor EF-G, by recording the fluorescence signatures of nine different reporters placed on both ribosomal subunits, tRNA and mRNA. We captured an early forward swiveling of the SSU head taking place while the SSU body rotates in the opposite, clockwise direction. Backward swiveling of the SSU head starts upon tRNA translocation and continues until the post-translocation state is reached. This work places structures of translocation intermediates along a time axis and unravels principles of the motions of macromolecular machines.

    >>>>>>

    Care to comment further?

    KF

  122. 122

    .
    Hello OLV,
    Thank you for the links. I will look them over.
    I miss hearing from GP as well.

  123. 123
    kairosfocus says:

    PA, the objections in the thread tell their own story on the powerful import of recognising that the genetic code is a manifestation of language and algorithms in a communication system and associated machine language controlled assembly units. Wiki’s admissions against interest are also significant. BTW, the protein synthesis diagram above comes from Wiki. KF

  124. 124
    daveS says:

    KF,

    Now that the Dionisio collective has arrived, this is shaping up to be quite the donnybrook.

    But more seriously, I will be interested to see whether this work comes to be regarded as an ID breakthrough among the wider ID community. If it is reported as such in other ID blogs and in ID journals, a heads-up would be appreciated.

  125. 125
    hazel says:

    kf writes, “H, I refer you again to the OP, starting with Crick’s letter; cf, 90 above. It is you who personalised and dismissed an argument tracing to a Nobel prize winner and on the prize winning work, to me the better to dismiss as “old.” ”

    kf, the Crick letter was in 1953, which was 66 years ago. That is old. I wasn’t dismissing any of the information you posted in the OP. I was just saying that was all information that people have known for a fairly long time, and that the argument that the genetic code and mechanism were designed had been around for a while.

  126. 126
    hazel says:

    Also, read this carefully, kf: DNA is a code. I never said it wasn’t. You appear to be constitutionally unable to make distinctions when you you think your beliefs are threatened. Also, read this: I AM NOT ARGUING AGAINST THE IDEA THAT DNA IS DESIGNED.

    Hope that makes that clear.

  127. 127
    kairosfocus says:

    H, once DNA is a code, it is a linguistic phenomenon. Further, one key aspect is that DNA contains algorithms expressed in code to create proteins. Thus we have language used in goal-directed purposes, i.e. the genome itself is a strong sign of design. I will just note that you clearly used “old” above dismissively, reframing the argument as though it were my idiosyncratic, dubious, long since discredited musings; and no it may be or may not be language in 85 does not get you off the hook when you are dealing with well established findings that the genetic code is just that, a code — no one argues that 2 + 2 may or may not equal 4 or that New York may or may not be a city on the Eastern seaboard of the USA. Pointing out its actual provenance is therefore a proper corrective. I add that your remarks about my beliefs being threatened are again resort to unwarranted personalisation. KF

    PS: Notice, in the OP I noted on the significance of reference to RE-cod[ing] as integral to the work done. This linguistic effort is part of the design work done by the investigators, then duly peer reviewed and published in Nature. Not only the leading venue for scientific publication, but also the place where the DNA double helix was first published.

    PPS: I will add that the breakthrough character of the work, as noted in the OP is as follows:

    Where are we today, then?

    First, we have definitive demonstration of the intelligent design of a genome. Yes, they obviously have not created a de novo cell body (a much more difficult task), but we see that intelligent design of life here definitively passes the Newton test of observed actual cause. Further, we see that DNA functions as an information system in the cell, supporting the significance of this conceptual representation, based on Yockey’s work . . . [images follow]

  128. 128
    hazel says:

    kf writes, ” we see that DNA functions as an information system in the cell”

    We’ve known that for a long time, haven’t we, ever since the genetic code was discovered.

  129. 129
    kairosfocus says:

    F/N: I remind on Newton’s rules of scientific reasoning, as at 10 above:

    Rule I [[–> adequacy and simplicity]

    We are to admit no more causes of natural things than such as are both true [[–> it is probably best to take this liberally as meaning “potentially and plausibly true”] and sufficient to explain their appearances.

    To this purpose the philosophers say that Nature does nothing in vain, and more is in vain when less will serve; for Nature is pleased with simplicity, and affects not the pomp of superfluous causes.

    Rule II [[–> uniformity of causes: “like forces cause like effects”]

    Therefore to the same natural effects we must, as far as possible, assign the same causes.

    As to respiration in a man and in a beast; the descent of stones in Europe and in America; the light of our culinary fire and of the sun; the reflection of light in the earth, and in the planets.

    Rule III [[–> confident universality]

    The qualities of bodies, which admit neither intensification nor remission of degrees, and which are found to belong to all bodies within the reach of our experiments, are to be esteemed the universal qualities of all bodies whatsoever.

    For since the qualities of bodies are only known to us by experiments, we are to hold for universal all such as universally agree with experiments; and such as are not liable to diminution can never be quite taken away. We are certainly not to relinquish the evidence of experiments for the sake of dreams and vain fictions of our own devising; nor are we to recede from the analogy of Nature, which is wont to be simple, and always consonant to [398/399] itself . . . .

    Rule IV [[–> provisionality and primacy of induction]

    In experimental philosophy we are to look upon propositions inferred by general induction from phenomena as accurately or very nearly true, notwithstanding any contrary hypotheses that may be imagined, till such time as other phenomena occur, by which they may either be made more accurate, or liable to exceptions.

    This rule we must follow, that the arguments of induction may not be evaded by [[speculative] hypotheses.

  130. 130
    OLV says:

    KF(121):

    The text you highlighted in the abstract of the paper is very significant.

    Let’s quote it again:

    “stepwise movements of the tRNAs together with the mRNA”

    “This work places structures of translocation intermediates along a time axis and unravels principles of the motions of macromolecular machines.”

  131. 131
    kairosfocus says:

    OLV, indeed, this is directly a manifestation of the stepwise process of an algorithm, and to get there there is a lot of supportive work in the cell carried forward by many molecules, so that choreography is a very material observation. It seems we need to be retr5ained to see what is there, having been for so long been distracted or blinded by imposed ideologies. KF

  132. 132
    OLV says:

    KF,

    I noticed you distinguished the reference to macromolecular machines within the highlighted text.
    That’s a very important term that must be pointed at.

    The first word in the title of the paper raises serious questions: choreography is repeated in the abstract too.

    Are we aware if the meaning of those two terms and their serious implications?

  133. 133
    OLV says:

    Wikipedia again:

    Choreography is the art or practice of designing sequences of movements of physical bodies (or their depictions) in which motion, form, or both are specified. Choreography may also refer to the design itself.

  134. 134
    kairosfocus says:

    OLV, macromolecules is about in effect smart polymers, assembled as functional units, i.e. machines. That too is pregnant with significance, especially when joined to choreography as in protein synthesis as seen in the OP. Multiply by use of a string based coded unit as control tape. KF

  135. 135
    OLV says:

    KF,

    Regardless of how we look at the current state of affairs in biology research.
    This is like watching a basketball match between a professional team (ID) and a college team (Darwinian), the score showing 500 : 1 (one point scored early for devolutionary adaptation/microevolution). A couple of minutes left but the pro team keeps scoring 3-pointers at an increasing rate. Game over.

  136. 136
    OLV says:

    The weather forecast just gets worse by day for the anti-ID crowd.

    Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination
    Arjun Prabhakar, Junhong Choi, […], and Joseph D. Puglisi

    As the universal machine that transfers genetic information from RNA to protein, the ribosome synthesizes proteins with remarkably high fidelity and speed. This is a result of the accurate and efficient decoding of mRNA codons via multistep mechanisms during elongation and termination stages of translation. These mechanisms control how the correct sense codon is recognized by a tRNA for peptide elongation, how the next codon is presented to the decoding center without change of frame during translocation, and how the stop codon is discriminated for timely release of the nascent peptide. These processes occur efficiently through coupling of chemical energy expenditure, ligand interactions, and conformational changes.

    Multidisciplinary studies of translation dynamics in the last two decades have illustrated the intricate network of movements and interactions of this multicomponent machinery that result in the observed high fidelity of translation.

    doi: 10.1002/pro.3190

    Single-Molecule Fluorescence Applied to Translation.
    Review article
    Prabhakar A, et al. Cold Spring Harb Perspect Biol.

  137. 137
    OLV says:

    The negative reactions we see here are just part of the noise in the system. That’s expected.
    They’re usually barking up the wrong tree. 🙂

  138. 138
    Brother Brian says:

    OLV

    The negative reactions we see here are just part of the noise in the system.

    With respect, the only negative reaction has to do with KF’s characterization of this paper as “groundbreaking ID research”. If the paper follows on from the abstract, this is a remarkable piece of research. But it is not “groundbreaking” from the ID perspective. It is just the use of technology to do something that we knew was possible for a long time. It does nothing to advance the ID argument.

  139. 139
    EricMH says:

    @BB lol! You say ‘No’ and then repeat what I said 😀

    And you say we’ve known this is possible for a long time. So, you may not notice, but this makes KF’s argument even more compelling!

    1. We know human intelligence can create from scratch the genetic code, whether copying, refactoring or even coding new functionality.
    2. Nothing else in nature that we know of can do this.
    3. Therefore, by abductive reasoning, some intelligent agency at least as powerful as human intelligence created the natural genetic code.

    According to BB #1 is completely obvious and uncontroversial. #2 is similarly uncontroversial, nebulous claims of “evolution did it” don’t count as concrete causes. Thus, BB makes KF’s point #3 even stronger. Thanks BB!

  140. 140
    Brother Brian says:

    EricMH

    BB lol! You say ‘No’ and then repeat what I said

    Great minds think alike. 🙂

    And you say we’ve known this is possible for a long time. So, you may not notice, but this makes KF’s argument even more compelling!

    How so? My expectation of something “groundbreaking” is that it shifts a paradigm, or demonstrates something that was previously thought to be impossible. But, don’t get me wrong. I can accept this as groundbreaking in that it has done something never done before. My disagreement is calling it groundbreaking ID research. Nobody is suggesting that we didn’t know that we would be able to do this eventually. From an ID perspective, the “groundbreaking” qualifier should have been raised a couple decades ago when we knew that it was possible.

  141. 141
  142. 142
    kairosfocus says:

    H,

    You may be quite correct — and BTW, resistant bacteria are becoming appallingly common. Tour is working on an attack nanotech drill related to his molecular car with bbuckeyball wheels that just won the first international nanocar race.

    Let’s clip as linked:

    CRISPR technology is a simple yet powerful tool for editing genomes. It allows researchers to easily alter DNA sequences and modify gene function. Its many potential applications include correcting genetic defects, treating and preventing the spread of diseases and improving crops. However, its promise also raises ethical concerns.

    In popular usage, “CRISPR” (pronounced “crisper”) is shorthand for “CRISPR-Cas9.” CRISPRs are specialized stretches of DNA. The protein Cas9 (or “CRISPR-associated”) is an enzyme that acts like a pair of molecular scissors, capable of cutting strands of DNA.

    CRISPR technology was adapted from the natural defense mechanisms of bacteria and archaea (the domain of single-celled microorganisms). These organisms use CRISPR-derived RNA and various Cas proteins, including Cas9, to foil attacks by viruses and other foreign bodies. They do so primarily by chopping up and destroying the DNA of a foreign invader. When these components are transferred into other, more complex, organisms, it allows for the manipulation of genes, or “editing” . . . . CRISPRs: “CRISPR” stands for “clusters of regularly interspaced short palindromic repeats.” It is a specialized region of DNA with two distinct characteristics: the presence of nucleotide repeats and spacers. Repeated sequences of nucleotides — the building blocks of DNA — are distributed throughout a CRISPR region. Spacers are bits of DNA that are interspersed among these repeated sequences . . . .

    The genomes of various organisms encode a series of messages and instructions within their DNA sequences. Genome editing involves changing those sequences, thereby changing the messages. This can be done by inserting a cut or break in the DNA and tricking a cell’s natural DNA repair mechanisms into introducing the changes one wants. CRISPR-Cas9 provides a means to do so.

    Sounds like an editing oriented molecular nanotech tool to me. If the cap fits, wear it. Another design tool targeting editing of DNA. Showing thereby, feasibility of such editing using tools and techniques already accessible to us.

    Looks like a growing box of tools.

    KF

    PS: On the dark side, ponder nextgen biotech weapons. How are we going to control those potential horrors?

  143. 143
    OLV says:

    KF (142):

    Good point.

  144. 144
    hazel says:

    So kf, is all genetic manipulation by people ID breakthroughs?

    How about all this? https://www.ohsu.edu/xd/research/centers-institutes/embryonic-cell-gene-therapy-center/

  145. 145
    mike1962 says:

    It’s no stretch to call the DNA/ribosome/protein complex a “biological programming platform.”

    If some intelligence invented it, that intelligence is pretty damn clever. If blind purposeless nature did it, then blind purposeless nature has some explaining to do.

  146. 146
    kairosfocus says:

    H, insofar as there is an emerging wave of technologies supportive of serious re-engineering of cells, clearly they would all count, individually and collectively. Remember, the point is, the significant scope genetic manipulation of the cell, pointing to possibilities in the deep past of origins. KF

  147. 147
    hazel says:

    So how about this: https://www.britannica.com/science/chemical-synthesis

    Chemists synthesize chemical compounds that occur in nature in order to gain a better understanding of their structures. Synthesis also enables chemists to produce compounds that do not form naturally for research purposes. In industry, synthesis is used to make products in large quantity.

    Are these ID breakthroughs?

  148. 148
    Brother Brian says:

    KF

    Remember, the point is, the significant scope genetic manipulation of the cell, pointing to possibilities in the deep past of origins.

    What possibilities are you suggesting? The possibility that human like material intelligent beings created genomes using similar material technology, inserted them in phospholipid sacs, and let them go wild 3+ billion years ago? If you are going to propose this materialist mechanism, I would be willing to listen to you. The next step would be to look for evidence of this in the deep past.

    However, if you are suggesting that our ability to use materialist technologies to do this is evidence that we should accept a non-material cause (ie., God) as a viable cause just does not follow. Just because we can demonstrate that humans can build the pyramids does not lead credence to the proposal that other pyramids may be constructed by supernatural beings.

  149. 149
    mike1962 says:

    Hazel: Are these ID breakthroughs?

    It depends on what they do with them. The ability to create complex functional systems simply by synthesizing non-natural chemicals doesn’t seems likely. Or necessary. However, the ability to manipulate – “program” – the DNA/ribosome/protein complex holds great promise of design and implementation of biological systems using that very powerful and robust, existing platform. I have never encountered any evidence that blind natural processes are responsible for the creation of complex functional systems or platforms. If you have any, I would be interested in seeing it.

  150. 150
    Mimus says:

    Hmmm, might I suggest that the desperation with which you have jumped on this paper suggests ID’s failure as a project is really about the movements own merits and not much to do with ideological exclusion? When you have to stretch this hard to find a positive , and go all the way back to Crick show a “breakthrough” what does that tell you about the health of the movement?

  151. 151
    OLV says:

    ID is being confirmed by many new research papers

    Check this out:
    https://evolutionnews.org/2019/05/orderly-disorder-a-molecular-motor-regulated-by-idp/

    Many technological inventions made by conscious agents are intelligently designed (ID). Some of them could be breakthroughs.

    The case referenced in this OP was done by conscious agents (ID) and it was breakthrough.

    But we keep hearing noise around here. Lots of whining and barking up the wrong trees.

    Oh, well. What else is new?

  152. 152
    Mimus says:

    One of Dionissio’s clique of alt. accounts calling someone else “noise” is really something special!

  153. 153
    kairosfocus says:

    H, kindly watch James Tour’s vid lecture (note his apology on going too far with “liar”). You will see a lot about synthesis, molecular machines etc . . . this is the molecule car builder and race winner. He is showing where we are. I already noted, maybe 100 years give or take to synthesise a whole cell. But that’s if fundable, budget holders may veto the from scratch route on grounds it is cheaper to harvest from the already there. For historical examples, cf HM Treasury and the sad story of British army equipment c 1900 – 1975. I dare not give current RW cases as they may cut a bit close to home here. What I will say is defining adequate performance is prior to assessing cost-effectiveness of options of adequate performance. Defeat, excessively high casualties [= blood and tears] and economic stagnation [= tears] through ill-advisedly choking off growth catalysts are only some of the consequences of penny-pinching penny-wise, pound foolish budget policies. Budgets must not shape strategies! End of rant, it being budget season. KF

  154. 154
    kairosfocus says:

    BB, you obviously have not seen what ID researchers and analysts have explicitly stated since the mid 1980’s. Namely, that evidence of design of cell based life on earth [and we can add, of emerging capability to do the same in our molecular nanotech labs] is not decisive on identity and nature of designers: within/ beyond our observed cosmos. It is OBJECTORS to ID who have been so fixated on the incorrect natural vs supernatural dichotomy that they missed this, creating a strawman caricature. If you re-read [or have you ever read?] the UD Weak argument correctives, you will see how we explicitly drew on Plato in The Laws Bk X c 360 BC — yes, 2360 years ago now — to identify the correct dichotomy relevant to ID: natural [= blind chance and/or mechanical necessity] vs ART-ificial cause, techne, based on intelligently directed configuration. It is the fine tuning of the observed cosmos which obviously would point to design antecedent to our cosmos. The connexion is then that the fine tuning sets our observed cosmos to a deeply isolated operating point that facilitates C-chemistry, aqueous medium, cell-based, terrestrial planet in galactic habitable zone life. That traces to Hoyle and the resonance enabling C and O in the abundance we see, etc. Further to this, logic of being points to a necessary being world root at finite remove, and our being morally governed creatures [including in our thought life: undeniably known duties to truth, right reason, prudence, sound conscience, fairness/equity, justice etc] points to the need for such a world root to be inherently good to found such moral government. Of course, all of this has been pointed out ever so many times, just brushed aside, dismissed without good reason, ignored, distracted from through threadjacking, studiously scrolled past etc. It is all relevant and revealing as to the sorry state and guilty secrets of today’s post-/ultra-modern Western mind. KF

  155. 155
    kairosfocus says:

    Mimus,

    you have projected — a well known sign of cognitive dissonance. I will note for record what was explicitly noted in the OP:

    Where are we today, then?

    First, we have definitive demonstration of the intelligent design of a genome. Yes, they obviously have not created a de novo cell body (a much more difficult task), but we see that intelligent design of life here definitively passes the Newton test of observed actual cause. Further, we see that DNA functions as an information system in the cell, supporting the significance of this conceptual representation, based on Yockey’s work [illustrations follow]

    The demonstrated ability to do the genome scale design work is relevant to forcing those who have played ideological lockout games to reconsider or stand exposed.

    In short, breakthrough in the proper sense of piercing a line of resistance.

    The breakout (the operational stage beyond breakthrough) is what you are now experiencing. We have declared independence and we proceed to think and develop for ourselves beyond the lines that were set up as a kill zone. The old objections are now demonstrably irrelevant as intelligent design of cell based life forms at genome scale is now demonstrated, peer reviewed, prestige journal published fact. Newton’s rules have been met and we may freely proceed.

    Design here and now like this implies that there can be no arbitrary lockout on inferring similar or better design on traces from the past of origins found in the cell. Starting with genetic code, algorithms and associated choreographed execution machinery.

    Let’s list:

    1> Codes — language.

    2> Algorithms — goal directed, purposive processes.

    3> Execution machinery and systems choreographed to work together in automata, molecular nanotech — molecular nanotech systems engineering of stunning brilliance.

    All, well beyond the 500 – 1,000 bit threshold beyond which blind chance and/or mechanical necessity are utterly implausible.

    Out there somewhere, Will Paley’s ghost is laughing.

    KF

  156. 156
    Mimus says:

    The old objections …

    This is the problem, though. No one has ever objected to ID on the groundsv that designing biology would not be possible. So the news humans have made a little progress down this path does not address objections to ID.

    Unless your can (clearly and succinctly) point out specific objections that are dealt with by this study?

  157. 157
    kairosfocus says:

    Mimus, strawman again. Design has been repeatedly locked out ideologically. A demonstration of genome scale design of cell based life here and now shows actual cause, undercutting the ideological excuses for the lock-out. KF

  158. 158
    OLV says:

    here’s another one in this website:

    https://uncommondescent.com/intelligent-design/the-immune-cells-it-turns-out-have-secret-police/

    The biology-related research literature is flooded with an overwhelming avalanche of new publications that’s hard to keep track of and the volume seems to increase out of control. It’s complex functionality and functional complexity all around.

    Enjoy it!

    BTW, will the penny eventually drop for the objectors?

    🙂

  159. 159
    OLV says:

    KF,

    Someone I know just came back from a transatlantic cruise where he saw a guest presenter answering questions using the typical handwaving technique developed by magicians. Apparently it was pathetically discouraging to see such a gullible audience applauding those entertaining pseudoscience presentations filled with hogwash. Welcome to this world.

  160. 160
    Brother Brian says:

    KF

    BB, you obviously have not seen what ID researchers and analysts have explicitly stated since the mid 1980’s.

    ID “researchers” state this because they don’t want to admit publicly that the only designer they will accept is God.

    When plate tectonics was posited as the cause of mountain building the researches didn’t say that the mechanisms of plate tectonics is off limits. When Darwin proposed his theory of evolution he didn’t state that the mechanisms of its action was off limits. But when asked what the mechanisms behind ID we are told that we shouldn’t be asking that question. Asking these types of questions is how good science progresses.

  161. 161
    daveS says:

    KF,

    A demonstration of genome scale design of cell based life here and now shows actual cause, undercutting the ideological excuses for the lock-out.

    Can you give one specific example of such an ideological excuse that has been used to lock out ID, that will be undercut by this work? (Preferably in 50 words or less).

  162. 162
    kairosfocus says:

    DS, the lockouts are notorious. The fact as now demonstrated in such a venue has the direct effect of undermining. KF

  163. 163
    daveS says:

    KF,

    Can you please be specific?

  164. 164
    Brother Brian says:

    KF

    DS, the lockouts are notorious.

    You keep repeating this. How many ID research papers have been rejected for publication in peer reviewed journals? I have asked this before and the only response I ever get is that there would be no point submitting them because they wouldn’t be excepted. And the editors of BioComplexity, ID’s pet journal, aren’t being worked very hard given the very low number of papers published.

  165. 165
    ET says:

    Brother Brian:

    How many ID research papers have been rejected for publication in peer reviewed journals?

    Totally clueless. It isn’t about “ID research”. It is about doing SCIENTIFIC research and being allowed to reach a DESIGN inference if the evidence warrants it as it does with the discovery of the genetic code.

    Also there is still absolutely ZERO blind watchmaker research papers and ZERO scientific research that supports blind watchmaker evolution. And there isn’t a scientific theory of evolution by means of blind and mindless processes.

  166. 166
    ET says:

    Why the OP is correct:

    That’s TWO cases of an intelligent agency producing a genome from scratch. And still ZERO for nature doing so.

  167. 167
    ET says:

    Brother Brian:

    But when asked what the mechanisms behind ID we are told that we shouldn’t be asking that question.

    What a dolt. You are told that ID is NOT about the mechanisms. That is because we do NOT have to know the exact mechanism used in order to determine design exists. We don’t even know how many large artifacts were made- and those are things we should be able to reproduce. However design is a mechanism, by definition. So is “built-in responses to environmental cues”.

    Genetic algorithms use evolution by means of intelligent design to solve the problems they were intelligently designed to solve.

    That said, your side is all about the mechanism because that is what Darwin posited- mechanisms that could replace the designer requirement.

  168. 168
    kairosfocus says:

    BB, ad hominem abusive and in willful defiance of the facts on the ground since 1984. The fact is, that the design inference is a logical exercise, inference to a causal process on empirically tested, reliable signs. An inference to process, intelligently directed configuration as a material cause, is simply not the same as inference to candidate designers. In the case of the world of life, the evidence in hand actually supports that design of life is feasible for a designer within the cosmos. Notice, I have put on the table that likely in about 100 years, we will have done the deed of creating wholly synthetic cell based life, providing we can persuade budget holders. Of course, if we do not blow up the world in any one of several ways first. KF

    PS; On design “mechanisms.” Design uses methodologies not mechanisms; at first level, I suggest you look up TRIZ — and yes, that is a journal on a whole philosophy of design. Designers also use technologies, and the OP is in part about just that. Technologies that made feasible whole genome synthesis and successful testing in a new strain of bacterium. You have made an objection in the teeth of an actual live example. That speaks about the kind of objections you are making.

  169. 169
    kairosfocus says:

    ET, while BB is likely deliberately provocative, easy on the rhetorical voltage, please. KF

  170. 170
    Brother Brian says:

    KF

    the case of the world of life, the evidence in hand actually supports that design of life is feasible for a designer within the cosmos.

    Nobody is arguing against that. But surely a material designer using material tools, because that is all that can be inferred from this research, would leave some evidence behind.

    But if you want anybody to take ID as a serious possibility, somebody is going to have to propose some testable hypotheses with regard to the mechanisms used. “Poof” will not b taken seriously.

  171. 171
    ET says:

    Brother Brian:

    But surely a material designer using material tools, because that is all that can be inferred from this research, would leave some evidence behind.

    The DESIGN is such evidence.

    But if you want anybody to take ID as a serious possibility, somebody is going to have to propose some testable hypotheses with regard to the mechanisms used.

    We have. We have said exactly how to test the claim that something was the result of being intelligently designed. On the other hand no one has done so for evolution by means of blind and mindless processes. Probability arguments exist only because no one knows how to test those claims.

  172. 172
    kairosfocus says:

    BB, you misrepresent the matter again. there has been every effort, every misrepresentation, even ill-advised court action to lock out consideration that design is a feasible explanation of life and of body plans. Going further, you do not even acknowledge that design does not work by mechanisms but by methodologies and by technologies, where the point of the case in the OP is that here we have a direct example of what can be done. KF

  173. 173
    kairosfocus says:

    F/N: The main test for ID is not in doubt and has been stated above: show a case where functionally specific complex organisation and/or information in excess of 500 – 1,000 bits has been produced by blind chance and/or mechanical necessity without intelligent direction, and the basis of the design inference would instantly collapse. As a direct case, random document generation exercises have so far maxed out at about 10^100 short in implied configuration space size. And yes, simply soaking up and digitising sky noise and searching for coherent meaningful text strings of relevant length, 72 – 143 ASCII characters or using a zener driven white noise source digitised to give flat random numbers such as is used in modern lotteries, would be a test. Similarly, the equivalent of setting up 500 – 1,000 coins and shaking at random then testing for a similar text string that is coherent and functional. Goal-driven incremental progress such as in the notorious Weasel case, is not a good test, save as a manifestation of an inefficient design driven process. Those who keep on repeating the falsehood that the design inference is not testable, in the teeth of clear statements on the record for many years, are acting irresponsibly. KF

  174. 174
    PeterA says:

    KF @173:

    “Those who keep on repeating the falsehood that the design inference is not testable, in the teeth of clear statements on the record for many years, are acting irresponsibly.“

    Agree.

  175. 175
    PeterA says:

    Brother Brian @160:

    “When Darwin proposed his theory of evolution he didn’t state that the mechanisms of its action was off limits. “

    He proposed the wrong mechanism that still today doesn’t explain how to get a prokaryote or a eukaryote cell. He misinterpreted his observations, extrapolating them without any empirical evidence. That’s misleading pseudoscience. It took many years for ID-unfriendly scientists to admit that the Darwinian core formulation RV+NS lacked explanatory power in light of the latest discoveries in biology research.
    Things will continue to get worse for those outdated ideas. New research papers will point to the increasing difficulties encountered by the Darwinian ideas. That’s because the only valid explanation is design by a conscious agent. There’s no other game in town. Wake up and smell the flowers in the garden.

  176. 176
    Brother Brian says:

    KF

    Going further, you do not even acknowledge that design does not work by mechanisms but by methodologies and by technologies, where the point of the case in the OP is that here we have a direct example of what can be done.

    So, you are proposing that life on earth got started by physical beings, using physical technologies. How did these physical beings come into existence?

  177. 177
    kairosfocus says:

    BB, 160:

    When Darwin proposed his theory of evolution he didn’t state that the mechanisms of its action was off limits. But when asked what the mechanisms behind ID we are told that we shouldn’t be asking that question.

    I again underscore that design is by its nature not a mechanism but an intelligent act, one that directs configuration of parts or components or portions towards a goal. A Michaelangelo carves a flawed marble into a David. A Ford builds a car, An Edison investigates the many possible materials for his light bulb. The researchers above used computer controlled synthesisers, manipulators etc to compose a recoded genome and to insert same into an E coli bacterium, leading to Syn61.

    Accordingly, we discuss DETECTION of design on empirically observable, reliable signs (what has been a sticking point in the face of ideologically deeply entrenched refusal to consider as a serious possibility). We examine, reverse engineer and study actual or possible methods and methodologies. We study, explore, develop, improve techniques and technologies, including machines, instruments and tools.

    All of these are well known and none of them are mysteriously, arbitrarily forbidden by ID researchers or thinkers. Indeed, had judge Jones listened to him, he might have learned much from Scott Minnich and from gene knockout experiments on irreducible complexity in bacteria. For that matter gene knockouts are a major technique used to identify the function of genes.Similarly, Behe’s investigations on the interactions of malaria and drugs show the power of statistical and epidemiological tools in drawing out patterns and principles through observational studies. And more.

    Again, the first major line of resistance has been the issue of detecting the empirically credible presence of design, in cases where direct observation is infeasible. A familiar task in many fields, including forensics, archaeology [vs “natural”], medical studies, etc. Part of that has been refusal to entertain the possibility of design in ideologically sensitive contexts, relevant to OoL and origin of body plans. That is now decisively broken through, thanks to an emerging pattern of cases of actual designs such as the OP headlines.

    Of course, that also immediately shatters the talking point that somehow, mysteriously there is a pretence that one is forbidden to investigate “mechanisms.” Mechanisms is not relevant, but methods and technologies certainly are. Lo, behold: it is the demonstration of successful methods and technologies as reported in Nature, that breaks the ideological line of resistance.

    The breakthrough is real.

    And once design is at the table, the readily shown challenge of needle in haystack search challenge shows why blind chance and/or mechanical necessity are maximally implausible once the explicit or implied functionally specific, configurational information exceeds 500 – 1,000 bits. Namely atomic level search resources in the Sol system [~ 10^57 atoms] or the — the only actually — observed cosmos [~ 10^80 atoms] and timeline ~ 10^17 s since singularity are such that no appreciable fraction of such a config space can be blindly explored. Likelihood of blind search success falls to negligible levels.

    However, through insight, knowledge, skill and imagination, designers are known to be able to get configurations right or nearly so, then refine through test and development. This drastically cuts down search challenge and then enables incremental improvement. Which last can be by hill-climbing “evolutionary” steps up a slope of function. However, as the OP also illustrates, that then faces the challenge of bridging to other islands of functionality. This pattern being a natural result of the requisites of correct, matched properly arranged and coupled parts. Such as we may readily see from text here vs random gibberish: fhystucfjhp[79556vksaroxdfzested.

    (Notice, how the above shows that simple cases are reachable by chance, but complex ones are a different matter as the random document experiments show.)

    Again, we are at breakthrough.

    KF

  178. 178
    kairosfocus says:

    BB,

    The patterns of the broken through line of ideological resistance are predictable and are predictably fallacies of irrelevance.

    We have in hand a direct demonstration by actual case, that intelligent design using lab methods and techniques can carry out genome scale intelligent design. That needs to be frankly faced and acknowledged.

    Next, we see effective methods and technologies, which answers to what is the mechanism.

    Now, we are on to, but who designed the designers and its cousins.

    Irrelevant.

    From direct demonstration, we know designers exist, that design is possible, that it cannot then be arbitrarily ideologically ruled out and mischaracterised as religion — pronounced here as an epithet — dressed up in a lab coat. (That invites the highly relevant rejoinder that science, to preserve its integrity must turn from being atheism in a lab coat.)

    The chain of reasoning is, we identify empirically reliable signs of design. Thus, we can detect presence of design as process. As that process is about intelligently directed configuration, its presence warrants inference that relevantly capable designers were active. Just as with an arson or burglary investigation. This is not rocket science . . . a capital case of learning from expensive, successive mistakes.

    In that context, we have in hand already a milestone. That needs to be acknowledged, this is not rhetorical sink the battleship, any hole will do so pepper away.

    Once design is credible, candidates to be designers (much as arson suspects) can be considered. As we have shown molecular nanotech labs can do the work with suitable staff, methods, technologies and equipment, such a candidate is on the table. Whether by panspermia and seeding or presence of say an orbital platform. Those are just ideas as to how such could be. Another candidate is at a higher level, it is possible that the physics of our cosmos was, in Hoyle’s words, monkeyed with:

    >>[Sir Fred Hoyle, In a talk at Caltech c 1981 (nb. this longstanding UD post):] From 1953 onward, Willy Fowler and I have always been intrigued by the remarkable relation of the 7.65 MeV energy level in the nucleus of 12 C to the 7.12 MeV level in 16 O. If you wanted to produce carbon and oxygen in roughly equal quantities by stellar nucleosynthesis, these are the two levels you would have to fix, and your fixing would have to be just where these levels are actually found to be. Another put-up job? . . . I am inclined to think so. A common sense interpretation of the facts suggests that a super intellect has “monkeyed” with the physics as well as the chemistry and biology, and there are no blind forces worth speaking about in nature. [F. Hoyle, Annual Review of Astronomy and Astrophysics, 20 (1982): 16.]>>

    . . . also, in the same talk at Caltech:

    >>The big problem in biology, as I see it, is to understand the origin of the information carried by the explicit structures of biomolecules. The issue isn’t so much the rather crude fact that a protein consists of a chain of amino acids linked together in a certain way, but that the explicit ordering of the amino acids endows the chain with remarkable properties, which other orderings wouldn’t give. The case of the enzymes is well known . . . If amino acids were linked at random, there would be a vast number of arrange-ments that would be useless in serving the pur-poses of a living cell. When you consider that a typical enzyme has a chain of perhaps 200 links and that there are 20 possibilities for each link,it’s easy to see that the number of useless arrangements is enormous, more than the number of atoms in all the galaxies visible in the largest telescopes. [ –> 20^200 = 1.6 * 10^260] This is for one enzyme, and there are upwards of 2000 of them, mainly serving very different purposes. So how did the situation get to where we find it to be? This is, as I see it, the biological problem – the information problem . . . .

    I was constantly plagued by the thought that the number of ways in which even a single enzyme could be wrongly constructed was greater than the number of all the atoms in the universe. So try as I would, I couldn’t convince myself that even the whole universe would be sufficient to find life by random processes – by what are called the blind forces of nature . . . . By far the simplest way to arrive at the correct sequences of amino acids in the enzymes would be by thought, not by random processes . . . .

    Now imagine yourself as a superintellect working through possibilities in polymer chemistry. Would you not be astonished that polymers based on the carbon atom turned out in your calculations to have the remarkable properties of the enzymes and other biomolecules? Would you not be bowled over in surprise to find that a living cell was a feasible construct? Would you not say to yourself, in whatever language supercalculating intellects use: Some supercalculating intellect must have designed the properties of the carbon atom, otherwise the chance of my finding such an atom through the blind forces of nature would be utterly minuscule. Of course you would, and if you were a sensible superintellect you would conclude that the carbon atom is a fix. >>

    . . . and again:

    >> I do not believe that any physicist who examined the evidence could fail to draw the inference that the laws of nuclear physics have been deliberately designed with regard to the [–> nuclear synthesis] consequences they produce within stars. [“The Universe: Past and Present Reflections.” Engineering and Science, November, 1981. pp. 8–12]>>

    Another approach is perhaps best seen through John Leslie’s eyes:

    “One striking thing about the fine tuning is that a force strength or a particle mass often appears to require accurate tuning for several reasons at once. Look at electromagnetism. Electromagnetism seems to require tuning for there to be any clear-cut distinction between matter and radiation; for stars to burn neither too fast nor too slowly for life’s requirements; for protons to be stable; for complex chemistry to be possible; for chemical changes not to be extremely sluggish; and for carbon synthesis inside stars (carbon being quite probably crucial to life). Universes all obeying the same fundamental laws could still differ in the strengths of their physical forces, as was explained earlier, and random variations in electromagnetism from universe to universe might then ensure that it took on any particular strength sooner or later. Yet how could they possibly account for the fact that the same one strength satisfied many potentially conflicting requirements, each of them a requirement for impressively accurate tuning?” [Our Place in the Cosmos, The Royal Institute of Philosophy, 1998 (courtesy Wayback Machine) Emphases added.]

    AND:

    “. . . the need for such explanations does not depend on any estimate of how many universes would be observer-permitting, out of the entire field of possible universes. Claiming that our universe is ‘fine tuned for observers’, we base our claim on how life’s evolution would apparently have been rendered utterly impossible by comparatively minor alterations in physical force strengths, elementary particle masses and so forth. There is no need for us to ask whether very great alterations in these affairs would have rendered it fully possible once more, let alone whether physical worlds conforming to very different laws could have been observer-permitting without being in any way fine tuned. Here it can be useful to think of a fly on a wall, surrounded by an empty region. A bullet hits the fly Two explanations suggest themselves. Perhaps many bullets are hitting the wall or perhaps a marksman fired the bullet. There is no need to ask whether distant areas of the wall, or other quite different walls, are covered with flies so that more or less any bullet striking there would have hit one. The important point is that the local area contains just the one fly.” [Emphasis his.]

    Noting also Walker and Davies:

    In physics, particularly in statistical mechanics, we base many of our calculations on the assumption of metric transitivity, which asserts that a system’s trajectory will eventually [–> given “enough time and search resources”] explore the entirety of its state space – thus everything that is phys-ically possible will eventually happen. It should then be trivially true that one could choose an arbitrary “final state” (e.g., a living organism) and “explain” it by evolving the system backwards in time choosing an appropriate state at some ’start’ time t_0 (fine-tuning the initial state). In the case of a chaotic system the initial state must be specified to arbitrarily high precision. But this account amounts to no more than saying that the world is as it is because it was as it was, and our current narrative therefore scarcely constitutes an explanation in the true scientific sense.

    We are left in a bit of a conundrum with respect to the problem of specifying the initial conditions necessary to explain our world. A key point is that if we require specialness in our initial state (such that we observe the current state of the world and not any other state) metric transitivity cannot hold true, as it blurs any dependency on initial conditions – that is, it makes little sense for us to single out any particular state as special by calling it the ’initial’ state. If we instead relax the assumption of metric transitivity (which seems more realistic for many real world physical systems – including life), then our phase space will consist of isolated pocket regions and it is not necessarily possible to get to any other physically possible state (see e.g. Fig. 1 for a cellular automata example).

    [–> or, there may not be “enough” time and/or resources for the relevant exploration, i.e. we see the 500 – 1,000 bit complexity threshold at work vs 10^57 – 10^80 atoms with fast rxn rates at about 10^-13 to 10^-15 s leading to inability to explore more than a vanishingly small fraction on the gamut of Sol system or observed cosmos . . . the only actually, credibly observed cosmos]

    Thus the initial state must be tuned to be in the region of phase space in which we find ourselves [–> notice, fine tuning], and there are regions of the configuration space our physical universe would be excluded from accessing, even if those states may be equally consistent and permissible under the microscopic laws of physics (starting from a different initial state). Thus according to the standard picture, we require special initial conditions to explain the complexity of the world, but also have a sense that we should not be on a particularly special trajectory to get here (or anywhere else) as it would be a sign of fine–tuning of the initial conditions. [ –> notice, the “loading”] Stated most simply, a potential problem with the way we currently formulate physics is that you can’t necessarily get everywhere from anywhere (see Walker [31] for discussion). [“The “Hard Problem” of Life,” June 23, 2016, a discussion by Sara Imari Walker and Paul C.W. Davies at Arxiv.]

    Our cosmos is fine tuned in ways that facilitate C-chem, aqueous medium, cell-based, terrestrial planet in galactic habitable zone life. That means that biology and cosmology are inescapably integrated, hence we see exobiology tied to the search for exoplanets. Which last is telling us a lot about just how privileged and unusual our own Sol system is. So, the cosmological inference to design and the biological inference to design constrain our thinking.

    We have a cosmos in which by fine tuning cell based life is possible, and on our planet actual. We cannot rule such pout across the observed cosmos. So, the nanotech lab is a possibility though we do not presently have more than demonstration of a possibility. Duty to evidence does not rule out on ideological grounds. At the same time, we have reason to believe our cosmos was designed in ways that facilitate such life. This suggests such an intent on the part of a designer capable of building a cosmos. Again, this cannot be ruled out. Where also, there is good reason to reject infinite regress of successive causes. We have good reason to hold to a finitely remote root of reality that is independent of external causes, i.e. is a necessary being. An intelligent, necessary being with capability to be wellspring of the cosmos is a serious candidate root of reality. But that properly belongs over the border in logic of being, ontology.

    So, it is not that we cannot address or arbitrarily lock out the question, it is just that it belongs to another discipline; one, that you were most dismissive of when it was on the table. But, one that is capable of showing fairly significant results. Especially, when one factors in that we are morally governed creatures, starting with our rationality itself. That puts the IS-OUGHT gap on the table, which, post-Hume, points to the only level where it can be bridged without falling into ungrounded ought. The source of reality must be inherently good, fusing is and ought. A cosmos-designing, enormously powerful, inherently good, rational, intelligent necessary being is clearly on the table as a candidate.

    So, in the end, but where did any such come from is the tactic of pocketing then dismissing the milestone in hand. We have a pair of birds in the hand, worth a flock in the bush. Let us work with the evidence.

    KF

  179. 179
    kairosfocus says:

    F/N: It is worth the while to ponder Newton in his general scholium to Principia:

    . . . This most beautiful system of the sun, planets, and comets, could only proceed from the counsel and dominion of an intelligent and powerful Being. And if the fixed stars are the centres of other like systems, these, being formed by the like wise counsel, must be all subject to the dominion of One; especially since the light of the fixed stars is of the same nature with the light of the sun, and from every system light passes into all the other systems: and lest the systems of the fixed stars should, by their gravity, fall on each other mutually, he hath placed those systems at immense distances one from another.

    This Being governs all things, not as the soul of the world, but as Lord over all; and on account of his dominion he is wont to be called Lord God pantokrator , or Universal Ruler; for God is a relative word, and has a respect to servants; and Deity is the dominion of God not over his own body, as those imagine who fancy God to be the soul of the world, but over servants. The Supreme God is a Being eternal, infinite, absolutely perfect; but a being, however perfect, without dominion, cannot be said to be Lord God; for we say, my God, your God, the God of Israel, the God of Gods, and Lord of Lords; but we do not say, my Eternal, your Eternal, the Eternal of Israel, the Eternal of Gods; we do not say, my Infinite, or my Perfect: these are titles which have no respect to servants. The word God usually signifies Lord; but every lord is not a God. It is the dominion of a spiritual being which constitutes a God: a true, supreme, or imaginary dominion makes a true, supreme, or imaginary God. And from his true dominion it follows that the true God is a living, intelligent, and powerful Being; and, from his other perfections, that he is supreme, or most perfect. He is eternal and infinite, omnipotent and omniscient; that is, his duration reaches from eternity to eternity; his presence from infinity to infinity; he governs all things, and knows all things that are or can be done. He is not eternity or infinity, but eternal and infinite; he is not duration or space, but he endures and is present. He endures for ever, and is every where present; and by existing always and every where, he constitutes duration and space. Since every particle of space is always, and every indivisible moment of duration is every where, certainly the Maker and Lord of all things cannot be never and no where. Every soul that has perception is, though in different times and in different organs of sense and motion, still the same indivisible person. There are given successive parts in duration, co-existent puts in space, but neither the one nor the other in the person of a man, or his thinking principle; and much less can they be found in the thinking substance of God. Every man, so far as he is a thing that has perception, is one and the same man during his whole life, in all and each of his organs of sense. God is the same God, always and every where. He is omnipresent not virtually only, but also substantially; for virtue cannot subsist without substance. In him are all things contained and moved [i.e. cites Ac 17, where Paul evidently cites Cleanthes]; yet neither affects the other: God suffers nothing from the motion of bodies; bodies find no resistance from the omnipresence of God. It is allowed by all that the Supreme God exists necessarily; and by the same necessity he exists always, and every where. [i.e accepts the cosmological argument to God.] Whence also he is all similar, all eye, all ear, all brain, all arm, all power to perceive, to understand, and to act; but in a manner not at all human, in a manner not at all corporeal, in a manner utterly unknown to us. As a blind man has no idea of colours, so have we no idea of the manner by which the all-wise God perceives and understands all things. He is utterly void of all body and bodily figure, and can therefore neither be seen, nor heard, or touched; nor ought he to be worshipped under the representation of any corporeal thing. [Cites Exod 20.] We have ideas of his attributes, but what the real substance of any thing is we know not. In bodies, we see only their figures and colours, we hear only the sounds, we touch only their outward surfaces, we smell only the smells, and taste the savours; but their inward substances are not to be known either by our senses, or by any reflex act of our minds: much less, then, have we any idea of the substance of God. We know him only by his most wise and excellent contrivances of things, and final cause [i.e from his designs]: we admire him for his perfections; but we reverence and adore him on account of his dominion: for we adore him as his servants; and a god without dominion, providence, and final causes, is nothing else but Fate and Nature. Blind metaphysical necessity, which is certainly the same always and every where, could produce no variety of things. [i.e necessity does not produce contingency] All that diversity of natural things which we find suited to different times and places could arise from nothing but the ideas and will of a Being necessarily existing. [That is, implicitly rejects chance, Plato’s third alternative and explicitly infers to the Designer of the Cosmos.] But, by way of allegory, God is said to see, to speak, to laugh, to love, to hate, to desire, to give, to receive, to rejoice, to be angry, to fight, to frame, to work, to build; for all our notions of God are taken from. the ways of mankind by a certain similitude, which, though not perfect, has some likeness, however. And thus much concerning God; to discourse of whom from the appearances of things, does certainly belong to Natural Philosophy.

    KF

  180. 180
    Brother Brian says:

    KF

    Again, we are at breakthrough.

    Really? Let’s test that theory. If this “designed” bug got into the wild and survived, and this paper was never published, how would you use your claimed design detection procedure to conclude that this bug was designed as opposed to a wild strain?

  181. 181
    kairosfocus says:

    BB, red herring. KF

    PS: OP, again:

    Where are we today, then?

    First, we have definitive demonstration of the intelligent design of a genome. Yes, they obviously have not created a de novo cell body (a much more difficult task), but we see that intelligent design of life here definitively passes the Newton test of observed actual cause. Further, we see that DNA functions as an information system in the cell, supporting the significance of this conceptual representation, based on Yockey’s work [images follow]

  182. 182
    daveS says:

    KF,

    Any echoes of your argument elsewhere in the ID-sphere yet? I don’t see anything at Evolution News yet.

  183. 183
    Brother Brian says:

    KF

    BB, red herring. KF

    Does this mean that your proven design detection tools can’t distinguish between human designed E. coli and wild E. coli? This either means that your design detection tools (which have never been demonstrated) or your claim that this paper is groundbreaking ID research, is less than advertised.

  184. 184
    ET says:

    Brother Brian:

    Does this mean that your proven design detection tools can’t distinguish between human designed E. coli and wild E. coli?

    LoL! You don’t have a mechanism- other than intelligent design- capable of producing any E coli. So any and all design detection techniques would say that the wild strain was intelligently designed.

    How did these physical beings come into existence?

    Your ignorance of science, while amusing, is still meaningless. One step at a time. We can only study what we have.

  185. 185
    Brother Brian says:

    ET

    LoL! You don’t have a mechanism- other than intelligent design- capable of producing any E coli.

    I guess you didn’t get KF’s memo that ID doesn’t have mechanisms. 🙂

  186. 186
    ET says:

    Brother Brian:

    I guess you didn’t get KF’s memo that ID doesn’t have mechanisms.

    Design is a mechanism. Intentional agency volition is mechanism. “Built-in responses to environmental cues” was written about over 20 years ago.

    What KF was referring to is that ID is NOT about the mechanisms.

  187. 187
    Brother Brian says:

    ET

    What KF was referring to is that ID is NOT about the mechanisms.

    It doesn’t appear to be about anything.

  188. 188
    ET says:

    Brother Brian:

    It doesn’t appear to be about anything.

    To you, a willfully ignorant and scientifically illiterate troll, perhaps. But unlike blind watchmaker evolution, at least ID makes testable claims and as such is scientific.

  189. 189
    PeterA says:

    KF @177-179:

    Excellent! Thanks.

  190. 190
    PeterA says:

    ET,

    Your interlocutor Brother Brian doesn’t seem to be interested in discussing anything seriously.
    I understand that he can be used as motivation for writing more, so that the anonymous readers can understand the ID paradigm better. Perhaps that’s what KF does so well. Thus the rest of us benefit from reading his insightful commentaries.

    Long ago someone suggested the possibility that those folks like Brother Brian are intentionally recruited by this website in order to make the ID objectors look like a bunch of naively oblivious whiners. I don’t take that option seriously, but who knows? 🙂 if that’s really the case, then we should admit that Brother Brian does it very well and could deserve an Oscar for accurate representation of the intended character. 🙂

  191. 191
    kairosfocus says:

    BB,

    further red herrings.

    The matter on the table is proven demonstration of actual genome scale intelligent design. By actual case on the table, such design has a right to be considered as a known adequate cause.

    In that context, we may look at signs of design and their empirical reliability. To which the answer on FSCO/I is that there are in fact trillions of cases in point [the Internet, every nut and bolt, many other cases] where we know directly that it is a mark of design as key causal factor, and there are exactly zero actually observed cases of blind chance and/or mechanical necessity causing such FSCO/I: functionally specific, config based complex organisation and/or information.

    The comments and OP for this thread are cases in point, including your own comments.

    Where, given that the genome contains such coded information, that is already direct relevance, where there is a recoding that is beyond the 500 – 1,000 bit threshold in the case in view. We have here an observed case of FSCO/I in the genome known to be by design, trillions plus one published in Nature.

    The needle in haystack, island of function search challenge then provides a plausible reason why this is so, a causal want of adequate means vs demonstrated adequate means challenge in effect. So, we have excellent reason to pull back and ponder the original genome for cell based life and for body plans, and to therefore note that we have here a strong sign of design.

    Where, significantly, this is also about code, thus language and algorithms, which are also signs of intelligent cause by design.

    KF

  192. 192
    hazel says:

    Hmmm. Question about rhetoric: how does a red herring differ from a strawman? Following up on my post at 62 about strawmen, sometimes people just exclaim “red herring” without explaining why that is accurate, and it’s not obvious just what the “red herring” is referring to.

  193. 193
    ET says:

    hazel- Why isn’t up to the people making the original claim to show how it is accurate?

  194. 194
    kairosfocus says:

    H, a strawman is one type of red herring. Above, BB tried to shift focal topic to something which is distractive. The force of the original point stands established, an actual case of genome scale intelligent design, showing possibility by way of actual instance. Duly, published in Nature. KF

  195. 195
    PeterA says:

    Ok,

    Let’s make this clear once more (rephrasing KF’s comment @194):

    “BB tried to shift focal topic to something which is distractive”

    Why?

    Because…

    “The force of the original point stands established, an actual case of genome scale intelligent design, showing possibility by way of actual instance.”

    I mean, what else could he do?

    🙂

  196. 196
    daveS says:

    KF,

    a strawman is one type of red herring.

    It’s probably not the case that all strawmen are red herrings, though. Someone may be confused about what the actual argument is and ‘knock over a strawman’, without intending to draw attention away from the track of truth and towards an oil of ad hominem-soaked strawman.

  197. 197
    Brother Brian says:

    Hazel

    Following up on my post at 62 about strawmen, sometimes people just exclaim “red herring” without explaining why that is accurate, and it’s not obvious just what the “red herring” is referring to.

    Declaring an argument a red herring or a strawman is a well known , and lazy, debate tactic. When you do so, you are falsely trying to justify why you are not addressing the point raised.

  198. 198
    Brother Brian says:

    KF

    Above, BB tried to shift focal topic to something which is distractive.

    I was directly addressing your claim that this paper was groundbreaking ID research. Let me put it in a form that you seem to think makes your arguments more sound.

    1) Groundbreaking research tends to be research that focuses (narrows) our model of the real world.

    2) Mendelian genetics did this for evolution and focused our attention on means to explain his observations of population “genetics”.

    3) This led to our discovery and describing of DNA.

    4) The groundbreaking discovery of DNA further focussed (narrowed) or model of evolution.

    5) You are claiming that our ability to modify and synthesize a genome is groundbreaking ID research.

    6) If it is groundbreaking, how is it focussing (narrowing) the ID model of life?

    7) The most obvious and logical way that it could do this is to focus (narrow) ID research to the possible material means of design. Pushing a supernatural (AKA, God) means to the back burner until all avenues of a material explanation have been exhausted.

    8) The fact that ID researchers (including yourself) refuse to do this is because this would remove God from the ID equation. Much like we have largely removed blending inheritance and strict Lamarckian mechanisms as strong candidates as explanations for evolution.

    Cue the response claiming that this is a red strawman so that you can justify not addressing this.

  199. 199
    EricMH says:

    @BB where are you seeing ID trying to keep God in the equation? Some ID proponents, like Nagel, are atheists. Some are religious, so of course they think God is the best candidate for designer. However, you seem to be confusing what some individual ID proponents believe with the logical claim of ID itself. This is like confusing the weird Pythagorean cult beliefs with the mathematics they developed. The mathematics stands on its own. Same with ID. The mathematical and biological theory should be examined independently of what the individuals believe. Even if they think ID is a great way to bring God back into schools, or what have you.

    You’ve got to separate the idea from the person, and criticize the idea on its own merits or lack thereof.

  200. 200
    hazel says:

    This is probably a boiled herring, or maybe a red strawman, but once you have decided that life was designed, I don’t understand why it wouldn’t be reasonable to want to know more about how that happened, with some due respect for separating metaphysical speculations and ideas that might be empirically investigated.

  201. 201
    kairosfocus says:

    BB, you just doubled down on red herrings and strawmen. It is clear you are not addressing the substantial point in the OP, but rather are distracting from it (as was cautioned against). Here we go yet again on that point, now simply for record:

    Where are we today, then?

    First, we have definitive demonstration of the intelligent design of a genome. Yes, they obviously have not created a de novo cell body (a much more difficult task), but we see that intelligent design of life here definitively passes the Newton test of observed actual cause. Further, we see that DNA functions as an information system in the cell, supporting the significance of this conceptual representation, based on Yockey’s work [images follow] . . . . At this stage, we definitively know that using nanotech molecular biology and linked computational techniques it is feasible to construct a genome based on intelligently directed configuration. AKA, design.

    Therefore, intelligent design, as of right not sufferance, sits at the table for study on origin of life and of body plans.

    Where, we separately know on configuration space search challenge, that it is maximally implausible to construct in excess of 500 – 1,000 bits of functionally specific complex organisation and/or associated information . . . . We are now in a different ball game completely: Intelligent Design of life is demonstrated to be feasible and actual in the here and now, as of this investigation. Therefore, as of right, it is a serious candidate to explain what we see in the world of life; especially as regards origin of cell based life and origin of main body plans.

    Going forward, we are now a full-fledged independent school of thought.

    Nowhere have I suggested that these researchers were consciously setting out on an explicit, ID-supportive project. They simply managed to demonstrate the actual feasibility of intelligent design of a complete genome.

    Similarly, nowhere have I argued that design of cell based life by itself means the designer of cell based life on earth is an extra-cosmic entity. Indeed, I pointed out more than once that this point has been on the table from ID thinkers since the 1980’s, in fact in the first work, TMLO. Your strawman caricatures have fallen flat.

    Further, despite being pointed to the UD weak argument correctives, you show basic ignorance of the per aspect design inference filter. The first default is blind mechanical necessity, defeated by high contingency on closely similar initial conditions. The second default is blind chance, defeated by functional specificity based on configuration AND tied to it informational complexity beyond a 500 – 1,000 bit threshold.

    Thus, the reasonable defaults are defeated by FSCO/I, for reasons explained above. No reasonable person will accept a selectively hyperskeptical begging of the default question. There are three main explanatory factors and defaults are chosen so they will only yield a design inference when a false positive is maximally implausible. And in fact we know on trillions of cases that the filter is reliable.

    Objections fail again, and are another distraction from the fact on the table, intelligent design of a functional genome.

    KF

  202. 202
    kairosfocus says:

    DS, that would be simple misunderstanding not a fallacy of distraction. KF

  203. 203
    kairosfocus says:

    H, the reported study is a pointer on first steps towards one way it may possibly have been done, i.e. on how a molecular nanotech lab could do the deed. More interestingly, on how we may proceed to do the like. Somehow, it strikes me that the OP above does not show lack of interest in relevant design approaches. I have pointed out that design is about methods and technology, not mechanism; but that should be obvious. KF

  204. 204
    kairosfocus says:

    F/N: Just to spark some thinking, Wiki on TRIZ:

    TRIZ (/?tri?z/; Russian: ?????? ??????? ???????????????? ?????, teoriya resheniya izobretatelskikh zadatch, literally: “theory of the resolution of invention-related tasks”) is “a problem-solving, analysis and forecasting tool derived from the study of patterns of invention in the global patent literature”.[1] It was developed by the Soviet inventor and science-fiction author Genrich Altshuller (1926-1998) and his colleagues, beginning in 1946. In English the name is typically rendered as “the theory of inventive problem solving”,[2][3] and occasionally goes by the English acronym TIPS.

    Following Altshuller’s insight, the theory developed on a foundation of extensive research covering hundreds of thousands of inventions across many different fields to produce a theory which defines generalisable patterns in the nature of inventive solutions and the distinguishing characteristics of the problems that these inventions have overcome[4].

    An important part of the theory has been devoted to revealing patterns of evolution and one of the objectives which has been pursued by leading practitioners of TRIZ has been the development of an algorithmic approach to the invention of new systems, and to the refinement of existing ones.

    TRIZ includes a practical methodology, tool sets, a knowledge base, and model-based technology for generating innovative solutions for problem solving. It is useful for problem formulation, system analysis, failure analysis, and patterns of system evolution. There is a general similarity of purposes and methods with the field of pattern language, a cross discipline practice for explicitly describing and sharing holistic patterns of design.

    The research has produced three primary findings:

    problems and solutions are repeated across industries and sciences
    patterns of technical evolution are also repeated across industries and sciences
    the innovations used scientific effects outside the field in which they were developed

    TRIZ practitioners apply all these findings in order to create and to improve products, services, and systems.[5]

    A theory and school of reflective praxis on technological evolution by systematic innovation.

    Of course, this leads to the question, what is mind.

    KF

  205. 205
    Brother Brian says:

    KF

    Nowhere have I suggested that these researchers were consciously setting out on an explicit, ID-supportive project.

    I never said that you did. All I have been saying is that your claim that it is groundbreaking research for ID is nonsense. For it to be groundbreaking it has to provide a much clearer understanding of how ID functions. If you are going to say that this paper points to direct synthesis of DNA by material beings, using material equipment, as the best current explanation of life on earth, then I would agree that it is groundbreaking for ID. But given your track record of not addressing any arguments that are contrary to your opinions, I expect you to avoid addressing this as well.

  206. 206
    kairosfocus says:

    BB, we can simply read the thread above. Second, the fact remains that the published research is a case of intelligent design and synthesis of a genome, involving recoding. That fact is decisive, so that the longstanding ideological lockout is now dead. KF

  207. 207
    ET says:

    Earth to Brother Brian-

    The paper reports of an intelligent design of an organism’s genome. That’s TWO cases of an intelligent agency producing a genome from scratch. And still ZERO for nature doing so.

  208. 208
    Brother Brian says:

    So, I have KF and ET agreeing that a material designer, using material technology, is the best explanation for life on earth. Anyone else willing to jump on this bandwagon? With this shift away from a supernatural cause to a natural cause, maybe ID can start working on identifying evidence for the mechanisms used to realize these designs made by material beings.

  209. 209
    daveS says:

    Brother Brian,

    So, I have KF and ET agreeing that a material designer, using material technology, is the best explanation for life on earth.

    Finally, the ideological lockout is dead!

  210. 210
    kairosfocus says:

    BB [& attn DS], strawman again. What has been shown is that design as process explains as a valid explanation. On the evidence in front of us we know that a sufficiently advanced nanotech lab is adequate for life on earth but we have had this on the table since the mid 1980’s from leading ID theorists. We do not have sufficient warrant to conclude that the ancient equivalent of Venter et al is the actual designer or the only relevant designer. We also have a wider relevant body of evidence, that the cosmos is fine tuned in ways that facilitate C-Chem, aqueous medium, cell based life. This means we have signs pointing to an extra-cosmic design process that resulted in a cosmos that sets the stage for cell based life. This would require entities adequate to cause a fine tuned cosmos; by definition extra cosmic. KF

  211. 211
    daveS says:

    KF,

    What has been shown is that design as process explains as a valid explanation. On the evidence in front of us we know that a sufficiently advanced nanotech lab is adequate for life on earth but we have had this on the table since the mid 1980’s from leading ID theorists. We do not have sufficient warrant to conclude that the ancient equivalent of Venter et al is the actual designer or the only relevant designer.

    To be clear, I don’t claim that we do have such warrant.

    Rather, the ideological lockout of the material-designer-hypothesis is over. We now have a live example.

  212. 212
    kairosfocus says:

    DS, you know the issue is design as causal process. KF

  213. 213
    daveS says:

    Quite so.

  214. 214
    kairosfocus says:

    DS, one of the things that has amazed me for years is the assumption by many supporters of evolutionary materialism, that blind chance and/or mechanical necessity can write code and algorithms as well as assemble execution machinery AND a von Neumann self replication facility to go with the metabolic automaton. Empirical warrant, nil. Configuration space search challenge, vastly beyond astronomical. This seems to be yet another guilty ideological secret. KF

  215. 215
    daveS says:

    KF,

    I’ll have to let the evo-mats reply to that one.

    For my part, I have no evidence indicating that “””supernatural””” beings exist and are able to interact with the physical world. When I can determine conclusively that something has been designed, the designer is invariably a material being.

  216. 216
    Brother Brian says:

    KF

    BB [& attn DS], strawman again. What has been shown is that design as process explains as a valid explanation.

    This research does not conclude such a broad thing. It It can only be used to conclude that material beings, using material equipment on material chemicals might be a valid explanation. If you are willing to accept this then I can accept that this is a breakthrough in the non supernatural concept of ID.

  217. 217
    Brother Brian says:

    KF

    We also have a wider relevant body of evidence, that the cosmos is fine tuned in ways that facilitate C-Chem, aqueous medium, cell based life.

    Yes, the old “hole in the ground was finely tuned for the puddle” argument. Is it not more likely that C-Chem, aqueous medium, cell based life is the only type possible given the universe we find ourselves in.

    This means we have signs pointing to an extra-cosmic design process that resulted in a cosmos that sets the stage for cell based life. This would require entities adequate to cause a fine tuned cosmos; by definition extra cosmic.

    If the supernatural being (why don’t you just call it God?) is required to design the universe with the “finely tuned” characteristics necessary for life then you are admitting that the material designer creating life using material equipment and material chemicals isn’t the groundbreaking ID research you think it is.

  218. 218
    Brother Brian says:

    DaveS

    When I can determine conclusively that something has been designed, the designer is invariably a material being.

    Quite so. And given that every material being we have ever observed had a beginning, the only logical inference is that this being also had a beginning. Does this mean that God created this first being, who then created all other living beings? But since this would require God to interact with the material world, which would make him a material being as well.

    My brain hurts.

  219. 219
    kairosfocus says:

    BB, yet more strawmen; here an utterly inapt claimed analogy. Cosmological fine tuning is a serious issue, highlighted originally by Hoyle on seeing an issue as to why C and O have the abundance they do, leading to finding the resonance responsible. Further, there is the problem of the unjustified default, i/l/o empirically linked reasoning. That is precisely why Newton highlighted the four rules of reasoning. In that context, the case reported in the OP shows that intelligent design of a genome is feasible. On trillions of test cases, FSCO/I is a reliable sign of design, one backed by the linked search challenge. Where, there are precisely zero observed cases of such FSCO/I coming about by blind chance and/or mechanical necessity. So the imposition of a presumption that what faces a search challenge barrier and has never been observed to achieve an effect is to be preferred is a mark of Lewontin’s question-begging ideological imposition, not cogent empirically grounded reasoning. That’s what ET has repeatedly pointed out. KF

    PS: Luke Barnes’ review on cosmological fine tuning here may be helpful. I note, again, that a design inference [i.e. to a causal factor] at cosmological level is not the same as inference to God as designer. The logic of being, addressing root of a world with morally governed creatures is a different argument from a different discipline — ontology etc — and it does point to the need for a necessary being world root that is inherently good in the moral sense, on pain of our rationality falling under grand delusion. That is not a design inference type of argument.

  220. 220
    kairosfocus says:

    F/N: The assumption that designers we observe are “material” beings, is seriously problematic. First, as there is no good reason to infer that all designers can only be embodied entities (and the fine tuning issue is a good excample there). Second, it is easy to show that a computational substrate processes information per mechanical necessity, programming and organisation, and/or blind chance, this does not have the characteristics required for rational inference. So, again, on pain of grand delusion, we have no good reason to infer that for instance we are wholly material creatures such that matter and its organisation account for our rational powers including those that allow us to be designers. The materialistic ideological assumption fails again. KF

    PS: A reminder, from Reppert:

    . . . let us suppose that brain state A [–> notice, state of a wetware, electrochemically operated computational substrate], which is token identical to the thought that all men are mortal, and brain state B, which is token identical to the thought that Socrates is a man, together cause the belief [–> concious, perceptual state or disposition] that Socrates is mortal. It isn’t enough for rational inference that these events be those beliefs, it is also necessary that the causal transaction be in virtue of the content of those thoughts . . . [But] if naturalism is true, then the propositional content is irrelevant to the causal transaction that produces the conclusion, and [so] we do not have a case of rational inference. In rational inference, as Lewis puts it, one thought causes another thought not by being, but by being seen to be, the ground for it. But causal transactions in the brain occur in virtue of the brain’s being in a particular type of state that is relevant to physical causal transactions.

  221. 221
    daveS says:

    KF,

    So, again, on pain of grand delusion, we have no good reason to infer that for instance we are wholly material creatures such that matter and its organisation account for our rational powers including those that allow us to be designers. The materialistic ideological assumption fails again.

    FTR, I do not infer we are wholly material beings. Just that we have a material component. And I have never encountered a wholly immaterial being designing or building anything.

  222. 222
    Brother Brian says:

    KF

    The assumption that designers we observe are “material” beings, is seriously problematic. First, as there is no good reason to infer that all designers can only be embodied entities…

    1) All confirmed examples of design are the result of an intelligent being (humans). From this you consider it a strong and valid inference to conclude that life is also the result of an intelligent being. Let’s call him God for the lack of a better word.

    2) All confirmed designers are known to be embodied entities. From this you do not consider it a valid interference to conclude that all designers are embodied beings.

    I agree that one of these inferences is stronger than the other. One compares apples and apples. One compares apples and dragon fruit. Your claim that your inference is valid and mine is not is just not speaking with regard to truth.

  223. 223
    kairosfocus says:

    BB,

    There is a reason why GIGO is a famous computer acronym: garbage in, garbage out.

    That is, a computational substrate is a blind, non-rational, machine entity, driven and controlled by mechanical necessity and/or chance, filtered through how it happens to be organised and programmed to react to inputs and/or stored information. As a result it will blindly output the result of the dynamics at work, leading to GIGO.

    In short, it is inherently incapable of the rational freedom and reflective insight required for reasoning, as Reppert so pointedly highlighted. That holds for digital computers, analogue ones, neural networks and more. The machine neither knows nor cares what it does, it is the designer, programmer and user who care.

    Therefore, we face a dilemma i/l/o our reflexivity: either our rationality and responsible freedom are real and we are living examples of mind beyond matter, or we are captive to a grand delusion bringing our rationality crashing to the ground. In which case, reasoned discussions are delusional, all reduces to manipulation.

    In short, nihilist absurdity and chaos . . . which, unfortunately, seems to explain all too well the motives and behaviour patterns of far too many of those who dominate policy, politics, media, education, the arts, culture, business, finance, government and law. Which, is part of why I have serious doubts about the sustainability of our civilisation i/l/o current trends.

    Alex Rosenberg sums up the materialistic view from the inside:

    Alex Rosenberg as he begins Ch 9 of his The Atheist’s Guide to Reality:

    >> FOR SOLID EVOLUTIONARY REASONS, WE’VE BEEN tricked into looking at life from the inside. Without scientism, we look at life from the inside, from the first-person POV (OMG, you don’t know what a POV is?—a “point of view”). The first person is the subject, the audience, the viewer of subjective experience, the self in the mind.

    Scientism shows that the first-person POV is an illusion. [–> grand delusion is let loose in utter self referential incoherence] Even after scientism convinces us, we’ll continue to stick with the first person. But at least we’ll know that it’s another illusion of introspection and we’ll stop taking it seriously. We’ll give up all the answers to the persistent questions about free will, the self, the soul, and the meaning of life that the illusion generates [–> bye bye to responsible, rational freedom on these presuppositions].

    The physical facts fix all the facts. [–> asserts materialism, leading to . . . ] The mind is the brain. It has to be physical and it can’t be anything else, since thinking, feeling, and perceiving are physical process—in particular, input/output processes—going on in the brain. We [–> at this point, what “we,” apart from “we delusions”?] can be sure of a great deal about how the brain works because the physical facts fix all the facts about the brain. The fact that the mind is the brain guarantees that there is no free will. It rules out any purposes or designs organizing our actions or our lives [–> thus rational thought and responsible freedom]. It excludes the very possibility of enduring persons, selves, or souls that exist after death or for that matter while we live.>>

    In short, evolutionary materialistic scientism is self-referentially absurd and necessarily self-falsifying, thus its current domination of thought and cultural agenda is ruinous.

    We need to start thinking afresh, from different premises that leave room for responsible, rational freedom, AND for our brains and CNS’s to be reasonably credible.

    For, though he meant to only use it to attack abstract thought that runs counter to his evolutionism, Darwin was right in his monkey brains remark in his famous letter to William Graham:

    . . . But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind? [To William Graham 3 July 1881]

    Haldane made much the same point in a famous 1932 remark:

    “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. 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. (NB: DI Fellow, Nancy Pearcey brings this right up to date (HT: ENV) in a current book, Finding Truth.)]

    Just to hammer the point home, here is Martin Cothran at ENV:

    The materialist, said Chesterton, “is not allowed to admit into his spotless machine the slightest speck of spiritualism or miracle.” Materialists like Harris keep asking why we make the decisions we do, and what explanation there could be other than the physiological. The answer, of course, is the psychological, the philosophical, the whimsical, and about a thousand others.

    But these violate the central tenets of his narrow dogma, and so are automatically rejected.

    There is something ironic about the position of thinkers like Harris on issues like this: they claim that their position is the result of the irresistible necessity of logic (in fact, they pride themselves on their logic). Their belief is the consequent, in a ground/consequent relation between their evidence and their conclusion. But their very stated position is that any mental state — including their position on this issue — is the effect of a physical, not logical cause.

    By their own logic, it isn’t logic that demands their assent to the claim that free will is an illusion, but the prior chemical state of their brains. The only condition under which we could possibly find their argument convincing is if they are not true. The claim that free will is an illusion requires the possibility that minds have the freedom to assent to a logical argument, a freedom denied by the claim itself. It is an assent that must, in order to remain logical and not physiological, presume a perspective outside the physical order.

    And this is not only a mortal consequence for Harris as the one trying to prove his point, it is also problematic from the reader’s perspective: If we are convinced by Harris’s logic, we would have to consider this conviction as something determined not by the rational strength of his logic, but by the entirely irrational arrangement of the chemicals in our brains. They might, as Harris would have to say, coincide, but their relation would be completely arbitrary. If prior physical states are all that determine our beliefs, any one physical state is no more rational than any other. It isn’t rational or irrational, it just is.

    If what Harris says is true, then our assent to what we view as the rational strength of his position may appear to us to involve our choice to assent or not to assent to his ostensibly rational argument, but (again, if it is true) in truth it cannot be any such thing, since we do not have that choice — or any other.

    Indeed, it is hard to see how, if free will is an illusion, we could ever know it. [“The Medial Pre-Frontal Cortex Did It: Sam Harris’s Free Will” by Martin Cothran at ENV (echoing C S Lewis and J B S Haldane etc) on November 9, 2012, HT the too often underestimated BA77, cf. here.]

    Clearly, reductio ad absurdum. We must turn to another, more promising approach.

    Where to begin?

    For one, we undeniably know that we are duty-bound to certain core duties of rational responsible freedom, indeed your own argument pivots on expecting us to be bound by these duties. That is to say, our inescapable duties to truth, to right reason, to sound conscience and to prudence, to fairness and justice, etc. Closely linked, we must see that we are in fact self-aware, conscious, reflective, self-moving, significantly free creatures and that these attributes cannot be on the whole grand delusion. Therefore, the computational substrate programmed by incremental blind chance and/or mechanical necessity through random variation (in the 47 or however many flavours) and differential reproductive success view of our rational life, decisively fails.

    In its place, we can consider the Eng. Derek Smith model of a two-tier controller, bio-cybernetic entity. That is, the brain and CNS are in-the-loop i/o elements, info stores etc in a cybernetic loop. However, they are also interfaced to a higher order controller that is supervisory. A suggested means of interface is quantum state influence, with heavy informational character. This opens up room for seeing another dimension that interacts with the material, the mental domain.

    We may then follow up on the import of our conscience-borne testimony: we are under a law of our nature: to the duties of rationality. We are morally governed, starting with our rationality. Thus, we face the notorious IS-OUGHT gap and Hume’s point that implies that such can only be bridged in the root of reality. That is, we need a necessary being world-root entity that is inherently good, so adequately rooting both the order of being and the order of duty.

    Where, BTW, a necessary being cannot be a composite entity assembled from separately existing component parts. Such a being is inherently composite and contingent; it cannot be necessary. A necessary being is required as causally independent of other things [= non-contingent] and framework to a world coming into being and being sustained. Recall, were there ever utter non-being, as such is without causal powers, non-being would forever obtain. As a world is, something always was, a necessary being world root. We have already had the long exchanges on why an infinite causal-temporal succession of the contingent is not a credible world root, as it involves the supertask of spanning the transfinite to reach to a finite span from now. We need a finitely remote, necessary (and so non-composite) being world root with power and wisdom to build a cosmos, also being inherently good to root a domain of responsible, rational, significantly free creatures.

    It is unfashionable to say or write such things today, but that does not undermine their force. Especially as we see the alternative, the nihilistic chaos and absurdity of the evolutionary materialistic scientism worldview. It is self-refuting by reduction to absurdity.

    Let us go on.

    Further to the above, after centuries of worldview level debates, there is precisely one candidate to be that world root: the inherently good, utterly wise, powerful creator God, a necessary and maximally great being. One, worthy of our loyalty and of the reasonable, responsible service of doing the good that accords with our evident nature.

    So, by taking the reality of responsible, rational, significantly free embodied designers seriously, we can see good reason to hold that the rationality itself implies that the materialistic world picture fails. Fails, as we cannot reduce mind to GIGO-limited blind computation on a material substrate. And even that substrate is not credibly the result of blind forces organising and programming it.

    The dominant ideology of our day is absurd, we need to turn to a view that comports with the manifest facts of responsible rational freedom.

    Ironically, we do not here have an inference TO designer but an inference FROM ourselves as embodied, brain-using creatures who are designers.

    In short, your argument above runs back ways and fails to address the absurdities of attempted materialistic models of mind.

    KF

  224. 224
    Brother Brian says:

    KF@223, that is a lot of words that do absolutely nothing to address my comment at 222. Let’s try again.

    1) All confirmed examples of design are the result of an intelligent being (humans). From this you consider it a strong and valid inference to conclude that life is also the result of an intelligent being. Let’s call him God for the lack of a better word.

    2) All confirmed designers are known to be embodied entities. From this you do not consider it a valid interference to conclude that all designers are embodied beings.

    Why is inference one a valid one and inference two is not?

  225. 225
    kairosfocus says:

    BB. your dismissive attempt fails. The fact of rational, responsible, significantly free– those factors are critical — embodied designers points to reality going beyond a world in which mind is reduced to GIGO-bound computational substrates. The latter reduces to absurdity — including wrecking inductive reasoning, which you tried to use to bind mindedness to GIGO-bound, inherently non-rational computational substrates — and starting over from the facts of rational consciousness (the basis for us to be designers) runs into the implications of such mindedness being inescapably under moral government through duties to truth, right reason, sound conscience and prudence, fairness and justice etc. Namely, that mind IS and is necessarily governed by OUGHT. So, for a credible mind to be, the IS-OUGHT gap must be bridged; which is only possible with an inherently good, necessary being world root. You can have a credible mind or you can try to reduce mind to epiphenomena of a GIGO-bound, blind and inherently non rational, mechanical force and/or chance driven computational substrate, but not both. The latter rapidly reduces to absurdity. So, you got the argument precisely backward: the reality of embodied designers points to the field of reality not being reduced to what evolutionary materialistic scientism envisions. Worse, such reduces to self-falsifying absurdity. A world with credible, designing, morally governed minds is not merely physicalist. Your attempt to bind mind to GIGO-limited, inherently non-rational computational substrates fails. KF

  226. 226
    kairosfocus says:

    F/N: As it has obviously not been adequately attended to, Reppert again:

    . . . let us suppose that brain state A [–> notice, state of a wetware, electrochemically operated computational substrate], which is token identical to the thought that all men are mortal, and brain state B, which is token identical to the thought that Socrates is a man, together cause the belief [–> concious, perceptual state or disposition] that Socrates is mortal. It isn’t enough for rational inference that these events be those beliefs, it is also necessary that the causal transaction be in virtue of the content of those thoughts . . . [But] if naturalism is true, then the propositional content is irrelevant to the causal transaction that produces the conclusion, and [so] we do not have a case of rational inference. In rational inference, as Lewis puts it, one thought causes another thought not by being, but by being seen to be, the ground for it. But causal transactions in the brain occur in virtue of the brain’s being in a particular type of state that is relevant to physical causal transactions.

    That inference on rational insight is morally governed as already described: duties to truth, right reason, sound conscience and prudence, fairness and justice etc. What kind of world must this be, to bridge the requisite IS and OUGHT? ANS: A world with a necessary being world root of inherently good character. As was already explained (but which was brushed aside rhetorically).

    KF

  227. 227
    Brother Brian says:

    KF@223, 225 and 226, I have never seen anyone expend so much energy to avoid answering a question. From this I can only assume that you realize that my inference is stronger than the design inference, and you don’t like it.

  228. 228
    kairosfocus says:

    BB, you are playing rhetorical games of evasion and polarisation. The fact is, you have tried to pin mindedness and conscious, responsible, significantly free mind to embodied computational substrates. The key factual and logical blunders in that exercise are that computational substrates are inherently non-rational, and that your argument is necessarily self-referential. So, if it is true we have no credible means of warranting it, because reduction of mind to computational substrates blows up rationality itself. On the contrary to your fallacious reasoning, we freely start from there being embodied, rational, responsibly free designers and ask, what kind of world has such; has room for credible rationality? The answer is, a world that is not what self-refuting evolutionary materialistic scientism envisions. So, the material fact is not, that we observe certain embodied designers, but that we observe conscious, conscience-guided, credibly responsibly and rationally free designers. This means that designers operate on both sides of the IS-OUGHT gap, and we live in a world where it is properly bridged, on pain of reducing rationality to grand delusion. Such a world will have in it an inherently good, necessary being world root. But of course, those locked into evolutionary materialistic scientism are strongly disinclined to follow much less take seriously such reasoning. Your reactions above are unfortunately diagnostic and telling about how the evolutionary materialistic crooked yardstick warps ability to reason. KF

  229. 229
    Brother Brian says:

    KF

    BB, you are playing rhetorical games of evasion and polarisation.

    Have you read your responses at 223, 225 and 226? Those are the biggest examples of evasion that I have seen in a long time.

    The fact is, you have tried to pin mindedness and conscious, responsible, significantly free mind to embodied computational substrates.

    No. I have provided an inference, based on billions of observations (ie, all examples of confirmed designers are embodied individuals), that you refuse to accept as a valid inference because it is more logically sound than the ID inference.

    The key factual and logical blunders in that exercise are that computational substrates are inherently non-rational, and that your argument is necessarily self-referential. </blockquote/
    If this is true of my inference then this means that humans (embodied beings) are inherently non-rational. Which means that the ID inference, which is based on comparisons to humans, is necessarily self-referential.

  230. 230
    daveS says:

    Brother Brian,

    I have never seen anyone expend so much energy to avoid answering a question.

    Indeed. We’re witnessing a veritable clinic on strawmen and red herrings here.

  231. 231
    kairosfocus says:

    DS (attn BB): I have long since answered the question, in detail and then in correction to onward doubling down.

    1: I did so by showing that the question pivots on a fundamental,. worldview level fallacy of self referential incoherence, which falsifies its implicit premises and leads to a very different association, that design pivots on morally governed rationality and thus points onward to a different sort of world than is envisioned by evolutionary materialists — whose view is self defeating. Namely,

    2: the fact of embodiment is not what drives design but the fact of responsible rational freedom, which latter is beyond what any computational substrate can do of its own inherently non-rational dynamical GIGo-limited functionality.

    For reference, I again point to Reppert — at this stage, simply for record:

    . . . let us suppose that brain state A [–> notice, state of a wetware, electrochemically operated computational substrate], which is token identical to the thought that all men are mortal, and brain state B, which is token identical to the thought that Socrates is a man, together cause the belief [–> concious, perceptual state or disposition] that Socrates is mortal. It isn’t enough for rational inference that these events be those beliefs, it is also necessary that the causal transaction be in virtue of the content of those thoughts . . . [But] if naturalism is true, then the propositional content is irrelevant to the causal transaction that produces the conclusion, and [so] we do not have a case of rational inference. In rational inference, as Lewis puts it, one thought causes another thought not by being, but by being seen to be, the ground for it. But causal transactions in the brain occur in virtue of the brain’s being in a particular type of state that is relevant to physical causal transactions.

    Thus,

    3: there is an ontological error at stake: the presumption that embodiment explains or could ever explain mind. We see designers who are embodied, but the embodiment does not account for their ability to design, so trying to infer to embodiment as a characteristic of designing intelligence is ill-founded. Where,

    4: as such rationality is morally governed, it points to a necessary being world-root capable of sustaining that order of being, morally governed rationality and linked reasoning. Which,

    5: is itself rational and designing (consider here the fine tuned cosmos) and by being a necessary being, is not an embodied being made up from atoms or other independently existing components.

    The argument that designers are embodied as a suggested induction, fails, fails in multiple ways.

    KF

  232. 232
    Brother Brian says:

    KF

    DS (attn BB): I have long since answered the question, in detail and then in correction to onward doubling down.

    I honestly believe that you think you did. But I assure you, your responses have been nothing but evasion so as to not open the door on the possibility that your God is not the designer.

    It is very quite simple.

    1) The ID inference is based on comparison to incidences of known design (human). It extrapolates this to life, where design has not been confirmed. Hence, inference.

    2) Using the same example (human design) we can also say that all confirmed designs were caused by embodied beings.

    3) The most logical inference for this is that all designs are caused by embodied beings.

    I could have narrowed the inference to say that all designs are caused by humans, but I wanted to give you a little wiggle room.

  233. 233
    Brother Brian says:

    DaveS

    Indeed. We’re witnessing a veritable clinic on strawmen and red herrings here

    Being a leftist a/mat, I prefer the terms “strawpersons of indeterminabt gender” and “colorblind piscine like organisms”. 🙂

  234. 234
    kairosfocus says:

    F/N: It seems, given the above, I need to also point out the correlation vs causation problem. Here, Wikipedia is a helpful short summary:

    In statistics, the phrase “correlation does not imply causation” refers to the inability to legitimately deduce a cause-and-effect relationship between two variables solely on the basis of an observed association or correlation between them.[1][2] The complementary idea that “correlation implies causation” is an example of a questionable-cause logical fallacy, in which two events occurring together are taken to have established a cause-and-effect relationship. This fallacy is also known by the Latin phrase cum hoc ergo propter hoc (“with this, therefore because of this”). This differs from the fallacy known as post hoc ergo propter hoc (“after this, therefore because of this”), in which an event following another is seen as a necessary consequence of the former event.

    That on some presumably finite and limited sample we find an association between A and B may indeed suggest a possibility of causal relationship. But that is not enough, we need to find a plausible dynamical connexion also. Smoking correlates with cancer, but that by itself is not enough, and chemical harm was established. Wiki gives a counter example where hormone replacement therapy at first seemed to reduce heart attack risk but then further findings showed the opposite.

    In this context, the question is whether design is causally driven by or inseparable from embodiment. As there is a rational element, the role of computational substrates is implicit as this is viewed as the locus of rationality, whether brains or hoped for strong AI. So, there is an implicit proposed dynamical connexion.

    However, it fails, as computational substrates are inherently non-rational. As Reppert discusses and as can be further drawn out at length.

    Instead, a far more fruitful connexion is that design is rational, and rationality requires freedom, which is morally governed. This was drawn out above, but seems to be repeatedly brushed aside on the perception that it is evasive and/or irrelevant. Above there was even a loaded suggestion that I am speaking with disregard to truth.

    In fact, the matter posed is a worldview level question, on ontology of mind. Which was addressed. Computational substrates do not account for rationality, period. Rationality does not find its roots in embodiment and associated computational substrates. Instead, pursuit of rational freedom points to a need for an ontology that transcends the material and bridges the IS-OUGHT gap, given the moral government involved. That has world-root level import as was drawn out above; import that is distasteful to those committed to naturalistic ideologies and is apt to be dismissed by them. But the social psychology of their cognitive dissonance is irrelevant to the grounding of rational, responsible, significantly free, thus morally [rather than mechanically and/or stochastically] governed mind.

    Consequently, observing that certain designers are embodied does not entail that design and associated rationality are causally rooted in embodiment.

    KF

  235. 235
    kairosfocus says:

    BB, kindly see the just above i/l/o the further above. Motive mongering on your part does not answer to the underlying ontological issue. KF

  236. 236
    hazel says:

    Perhaps “God” is a combination of material and immaterial properties. Given that “material”, according to our current ideas, ultimately is quantum in nature, the source of our universe, “God”, might be a quantum being who is as much material as we are. but exists as a quantum whole in a level of reality beyond the world we live in. If we use both body and mind to design and create, the inference that similar beings exist which are also designers and creators is worth considering. BB’s question: why is this an invalid inference?

  237. 237
    Brother Brian says:

    KF

    BB, kindly see the just above i/l/o the further above.
    None of that addresses the validity of the inference I presented. ID keeps saying that a supernatural being isn’t required for ID.

  238. 238
    kairosfocus says:

    BB, you are doubling down on adequately corrected errors at this point. As to the design inference and design theory, have you as yet [again?] worked through the UD Weak argument correctives? If you had done so, you should not be arguing like that. KF

  239. 239
    daveS says:

    KF,

    I did so by showing that the question pivots on a fundamental,. worldview level fallacy of self referential incoherence, which falsifies its implicit premises and leads to a very different association, that design pivots on morally governed rationality and thus points onward to a different sort of world than is envisioned by evolutionary materialists — whose view is self defeating.

    Nonsense. No one is invoking the premises of “evolutionary materialism” here. It’s a straightforward inductive argument.

  240. 240
    kairosfocus says:

    H, you are opening up a huge domain, logic of being, philosophical theology and the idea of God, systematic theology, how such matters correlate with traditions. My comment is, above — as world root issues came up — I have spoken to such, including to what some call the God of the philosophers, here, God as conceived through the lens of root of being and through roots of morally governed being. Necessary beings are not made up from arrangements of proper parts, and God is understood to be such. As such God as to core nature is immaterial, spiritual and mental. In the Christian tradition he is also incarnate, which becomes a very powerful concept. But before that in him we live, move and have our being, he upholds all things by his word of power, without him was not anything made that was made. There is much more, thousands of closely reasoned pages worth. Too much for a blog comment. But if we are going to address rational, responsible, morally governed minded creatures, these subjects will open up. KF

  241. 241
    kairosfocus says:

    DS, no. The question exists in the context where embodiment and computational substrates are held to account for rationality. This fails, as shown. KF

  242. 242
    daveS says:

    As they say in some commonwealth countries, “bollocks”. You’re putting words in Brother Brian’s mouth.

  243. 243
    hazel says:

    Sorry, kf, bb, and ds: please ignore my comment.

  244. 244
    kairosfocus says:

    DS, the matter is clear on substance: there is no good reason to infer that designers must be or inevitably are embodied, on the nature of rationality as requiring freedom which is morally not mechanically governed. Inference to design, is not inference to embodied designers, and even if the designers are embodied, computational substrates do not — cannot — account for rational freedom to infer and warrant. Mind, to be credible, must be free and morally governed, it cannot be mechanically and/or stochastically governed as computational substrates are . . . as we both know in intimate detail down to device physics, up through circuits and networks to systems and architecture, taken not only on digital machines but analogue ones and neural networks. Good day. KF

  245. 245
    Brother Brian says:

    KF@244, you are still dodging the logical conclusion. If you are going to infer that life is designed because all known designs have an intelligent designer (a ludicrous inference to start with), then you also have to acknowledge the validity of the inference that all designers are embodied because all known examples of designers are embodied. If you dismiss one you have to dismiss the other.

  246. 246
    kairosfocus says:

    BB, no. Your argument fails, as was shown. Rationality required to be a designer is not bound to embodiment and associated computational substrates, as such substrates are non-rational and are mechanically and/or stochastically rather than morally governed. A key clue. Designers may be embodied but that does not rule out the possibility of those that are not. On the wider range of evidence, embodied designers are “amphibians.” KF

  247. 247
    Brother Brian says:

    KF

    Rationality required to be a designer is not bound to embodiment…

    And yet all known examples are embodied. Don’t blame me because the same type of inference that you use for ID rules out God as the designer.

    … and associated computational substrates, as such substrates are non-rational and are mechanically and/or stochastically rather than morally governed.

    Good example of goalpost shifting. The fact remains, all known examples of designers are embodied individuals. And what does moral governance have to do with being a designer? That doesn’t make any sense. Why can’t a completely amoral individual be a designer?

  248. 248
    kairosfocus says:

    BB,

    first, you confuse examples you accept as known and those known to others. Millions of people personally know God in positively life-transforming ways, for example. Or, are you willing to assign us to the category, deluded? If so, that comes with a stiff price, undermining credibility of mind — as the alleged delusion would be so widespread, so persistent, so pervasive, so indelible that it would rise to the level of grand delusion.

    We rely on the credibility of mind just to have an exchange. Absent utter demonstration otherwise, we take that credibility as a given. And indeed, a claimed demonstration otherwise would imply that demonstration itself is impossible. We deal here with inescapable truth.

    Next, let me point out that there is an issue of the principle of identity at work. Yes, that A is itself, A i/l/o its core, defining characteristics. Thus, when we see embodiment or composition as material, with computational substrates, we find certain properties and resulting capabilities/ performance. In particular, we see why computation is inherently a non rational, blind, mechanically and/or stochastically governed process. That is by contrast with intelligent action, which turns on understanding, insight, inference, freedom and duties to truth, right reason, prudence, fairness/justice etc. That is, it is morally governed.

    What we actually observe is:

    A: [material computational substrates] –X –> [rational inference]

    B: [material computational substrates] —-> [mechanically and/or stochastically governed computation]

    C: [intelligent agents] —-> [rational, freely chosen, morally governed inference]

    D: [embodied intelligent agents] —-> [rational, freely chosen, morally governed inference]

    The set of observations A through D imply that intelligent agency transcends computation, as their characteristics and capabilities are not reducible to:

    – components and their device physics,
    – organisation as circuits and networks [e.g. gates, flip-flops, registers, operational amplifiers (especially integrators), ball-disk integrators, neuron-gates and networks, etc],
    – organisation/ architecture forming computational circuits, systems and cybernetic entities,
    – input signals,
    – stored information,
    – processing/algorithm execution,
    – outputs

    This is what Reppert was getting at:

    . . . let us suppose that brain state A [–> notice, state of a wetware, electrochemically operated computational substrate], which is token identical to the thought that all men are mortal, and brain state B, which is token identical to the thought that Socrates is a man, together cause the belief [–> concious, perceptual state or disposition] that Socrates is mortal. It isn’t enough for rational inference that these events be those beliefs, it is also necessary that the causal transaction be in virtue of the content of those thoughts . . . [But] if naturalism is true, then the propositional content is irrelevant to the causal transaction that produces the conclusion, and [so] we do not have a case of rational inference. In rational inference, as Lewis puts it, one thought causes another thought not by being, but by being seen to be, the ground for it. But causal transactions in the brain occur in virtue of the brain’s being in a particular type of state that is relevant to physical causal transactions.

    It seems further, that you are unwilling to acknowledge that we all undeniably know that our rational life is governed through duties to truth, right reason, prudence, fairness/justice etc. And yet, the whole point of your attempts to argue is to persuade through your knowledge that we have these duties. The rejection of these duties transforms rationality into self-manipulation and manipulation of others through in the end cynical will to power. That is, we see reduction to the absurdity of nihilistic chaos and collapse of communicative rationality.

    An individual may indeed flout these principles through amoral, nihilistic will to power and manipulation. But in so doing, that agent is forced to rely on our adherence to these duties. That is, amorality and nihilism parasite off the general acknowledgement of these duties of rational freedom. Were that condition to become dominant, community rational life would collapse into chaos, both revealing it as an evil and underscoring the vital importance of such moral government. That Cretans are liars [when they think they can get away with it] cannot extend to Cretans are universally deceitful, or else Cretan community would collapse.

    Such moral government and underlying responsible freedom are essential components of rationality. We are undeniably morally governed (as an aspect of our freedom) and such would extend to any other intelligent agent.

    Where, further, the capabilities of rational, responsible freedom do not bind to embodiment or to material composition. They are a strong indicator of our “amphibian” character, manifest in the famous phrase: mind over matter. As such, we have no proper epistemic right to rule out that intelligent agency may operate independent of a material, computational or cybernetic substrate.

    As was already pointed out, the Smith model allows us to consider a cybernetic loop with a controller that is two-tiered. One is an in the loop computational substrate, the other a supervisor with purpose, freedom of action etc. The two have been envisioned as interacting through quantum inferences. We obviously do not understand how interactions happen, but we can and do recognise the necessity of responsible freedom for rationality and why computational substrates by themselves do not have that freedom.

    Just last night, driving home for a meeting in prep for onward budget debate, in the dark, I came to a strange-seeming fork in the road. It seemed the left was the better option, but then as I got closer I perceived that the right fork was the correct one to attain my purposes. I turned right, despite the lingering appeal of the left. Similarly, passing a nearby point earlier, I again saw what looked like a grazing animal (which I had seen many months before) but I recognised what I learned earlier, that this is an illusion created by a peculiar line of bushes. So, I superposed on my lingering perception, that this is an optical illusion and even briefly pondered some of why it works. Of course, routinely, similar illusions are artistically used in paintings and in videos. We willingly suspend our knowledge of an illusion, to perceive a message of verisimilitude. Though, with AI, the emergence of deep fakery can paint a desired face over a convincing but false image. Likewise, as I type, I make choices of composition, computers offering flexibility to readily edit on the fly.

    In all of these, the supervisory and computational come together but are perceptibly distinct. They have distinct identity and nature. Therefore, there is a general recognition of the distinction; save, among those committed to the self-referentially incoherent ideology of evolutionary materialism and their fellow travellers.

    The ideology fails, we freely follow the evidence of distinct identity and nature.

    KF

  249. 249
    Brother Brian says:

    KF

    BB,

    first, you confuse examples you accept as known and those known to others. Millions of people personally know God in positively life-transforming ways, for example.

    Well, this discussion has certainly taken a turn to the surreal.

    If I make an inference that all known designers are embodied beings therefore all designers are most likely embodied individuals, it is not valid because I haven’t taken God into account. But ID can make a very similar inference and claim that it is independent of God. Do you have your cake and eat it much?

  250. 250
    Ed George says:

    Although I generally side with KF over BB, I’m afraid that BB is correct here. KF just appears to be clutching at straws.

  251. 251
    kairosfocus says:

    EG:

    >>Although I generally side with KF over BB,>>
    — Manifestly false on long track record; stable-mate may be more like it.
    — Classic concern troll start-point.

    >> I’m afraid that BB is correct here.>>
    — Pile-on tactic
    — The substantial point remains clear: the case in the OP demonstrates that intelligent design at genome level is feasible (so also, that such intelligently directed configuration cannot be ideologically locked out in considering OoL or Oo body plans.
    — Said lockout is of course a notorious problem and you will scan above in vain to see acknowledgement of an outrageous pattern of academic, media, administrative and legal bias. Telling.
    — The operative factor being intelligence, and there being a notorious observation that there’s more than one way to skin a cat[fish], we are not bound to lock such intelligently directed configuration down to use of the sort of technologies used in this case.
    — There also being an attempt to bind the inference to the claim that designing intelligence in this case must be embodied, it is in order to observe why such is a case of post hoc reasoning, an error of observational bias or happenstance.
    — Notoriously, this pivots on brains as wetware, a neural network based form of computational substrate.
    — Accordingly, it is entirely in order to point out the nature of such a substrate, which is inherently non-rational, a mechanically and/or stochastically governed blind entity. Such is not intelligent and rational, regardless of what those wedded to strong AI may hope for.
    — By contrast, rationality is inherently free, insight-driven and morally governed through duties to truth, right reason, prudence (thus, warrant and caution etc), fairness and justice etc.
    — This, on pain of nihilistic collapse and absurdity . . . and even the manipulative nihilist parasites off our adherence to these duties.
    — There is therefore a sufficient difference of characteristics to properly infer a categorical distinction of nature and identity: mind over matter (which is widely understood save where evolutionary materialistic ideology warps thinking, this ideology being self-refuting on grounds tied to our present considerations)
    — Moral government also implies that mind inherently, inescapably acts on both sides of the IS-OUGHT gap, underscoring the need to bridge it.
    — This can only be done at world-root level, requiring that the necessary being world root [required on logic of being grounds] is adequate to ground moral government. Only an inherently good entity at world root can fill this bill.
    — And yes, this is a worldview level issue; that is inherent to what was asked. Worldview level question begging by ideological imposition of evolutionary materialistic scientism (which is self-refuting but institutionally dominant) undermines freedom to seek well warranted truth.
    — Unfortunately, just such imposition, is notoriously present and is one of the means by which the soundness of the mind of Western man has been radically undermined.

    >> KF just appears to be clutching at straws>>
    — More of the same piling on pattern.
    — If my argument is so utterly fallacious then kindly engage it on comparative difficulties and overturn it, rather than piling on on talk points.

    KF

  252. 252
    daveS says:

    KF,

    Rationality required to be a designer is not bound to embodiment and associated computational substrates

    Has anyone one claimed otherwise? I don’t believe so. This appears to be a strawman you are arguing against.

  253. 253
    kairosfocus says:

    BB,

    you question-beggingly lock out a world of observations again, and compound by highly loaded suggestions. It is simply not the case that there is a global consensus — never mind the radical secularists and their hall of mirrors — that all actually observed designers are embodied entities. Billions would and do beg to differ, and they cannot all be written off as delusional without self-referentially, radically undermining the credibility of human rationality.

    I think you do not realise that you crossed the border and are making a worldview level, philosophical claim with significant metaphysical import.

    That has to be handled on a very different base than projection from we observe embodied genetic engineers, a few thousands, so we infer that intelligently directed configuration of genes etc will be by similarly embodied creatures. The problem here is immediately the post hoc fallacy, leading to binding designing intelligence to embodiment (and to possessing a wetware computational substrate).

    I have pointed this out several times, going so far as to highlight the statistical blunder. Where, surely, you recognise that statistics is in material part mathematically structured inductive inference.

    I also addressed the ontological error, as, demonstrably, computation on a substrate is categorically distinct from free, rational, morally [not mechanically and/or stochastically] governed reasoning. That cuts across a lot of fashionable thinking today on AI etc. but is quite clear. Yet again — notice, how you have never answered this — Reppert:

    . . . let us suppose that brain state A [–> notice, state of a wetware, electrochemically operated computational substrate], which is token identical to the thought that all men are mortal, and brain state B, which is token identical to the thought that Socrates is a man, together cause the belief [–> concious, perceptual state or disposition] that Socrates is mortal. It isn’t enough for rational inference that these events be those beliefs, it is also necessary that the causal transaction be in virtue of the content of those thoughts . . . [But] if naturalism is true, then the propositional content is irrelevant to the causal transaction that produces the conclusion, and [so] we do not have a case of rational inference. In rational inference, as Lewis puts it, one thought causes another thought not by being, but by being seen to be, the ground for it. But causal transactions in the brain occur in virtue of the brain’s being in a particular type of state that is relevant to physical causal transactions.

    The obvious conclusion is, you don’t have a cogent reply.

    Let me address your latest claim in steps of thought:

    >>If I make an inference that all known designers are embodied beings>>

    a: Begs the question, billions for cause beg to differ.

    b: One cannot simply imply delusion on that scale, as it would undermine (self-referentially) the credibility of human rationality.

    c: In short, your first premise locks out any conclusion other than the one you wish and is dubious, highly debatable.

    d: Further to this, you have consistently failed to address the other design inference, fine tuning. This points to extra-cosmic designer.

    e: Yet further, the logic of being requires a finitely remote necessary being world root capable of causing a fine tuned C-Chem aqueous medium cell based life facilitating cosmos. Necessary beings cannot be composed of arranged, independently existing proper parts. That may be unfamiliar to you but is readily established as composite entities are inherently contingent.

    f: There is good reason to set aside your first premise and recognise instead that we observe designing intelligences so designing intelligence is possible. Without question-begging ontological commitments.

    >> therefore all designers are most likely embodied individuals,>>

    g: Reasoning on a begged question goes in pointless circles.

    h: Further, this side-steps the point I have elaborated above, on the known ideology at work across our civilisation, evolutionary materialistic scientism, i.e. you are setting up a strawman to knock over.

    i: On this ideology, intelligence is founded on sufficiently sophisticated computational substrates, but it is readily seen that these are blind, mechanically and/or stochastically governed glorified calculating engines, not responsibly and rationally free reasoning entities. Never mind pretentions of AI, they are inherently not freely thinking intelligences.

    j: Thus, it is an error to seek to bind intelligence to embodiment. Intelligences may indeed be embodied, but this points to an “amphibian” ontological character: mind over matter.

    k: I clip from above — which you ducked in order to revert to a compound fallacy now being answered point by point:

    What we actually observe is:

    A: [material computational substrates] –X –> [rational inference]

    B: [material computational substrates] —-> [mechanically and/or stochastically governed computation]

    C: [intelligent agents] —-> [rational, freely chosen, morally governed inference]

    D: [embodied intelligent agents] —-> [rational, freely chosen, morally governed inference]

    The set of observations A through D imply that intelligent agency transcends computation, as their characteristics and capabilities are not reducible to:

    – components and their device physics,
    – organisation as circuits and networks [e.g. gates, flip-flops, registers, operational amplifiers (especially integrators), ball-disk integrators, neuron-gates and networks, etc],
    – organisation/ architecture forming computational circuits, systems and cybernetic entities,
    – input signals,
    – stored information,
    – processing/algorithm execution,
    – outputs

    >> it is not valid because I haven’t taken God into account.>>

    l: Motive mongering, given widespread polarisation once “God” is mentioned.

    m: Above and previously, I have pointed out that billions will disagree, for cause, with the claim that ALL intelligences we have observed are embodied, i.e. I pointed to question-begging and further to the implications of implying such widespread delusion. Including, self-referential implications for you.

    n: Further, I have already taken much time and effort to mark the ontological differences between computational substrates and freely acting, insightful, morally governed intelligence. That counts and we scan above, in vain, for a cogent answer on your part.

    >> But ID can make a very similar inference>>

    o: You really need to read the UD weak argument correctives and take their points seriously, even if you disagree with our conclusions.

    p: The design inference is an inference on reliable signs, from observed functionally specific, sufficiently complex, configuration based organisation and associated information to a causal process . . . not agency . . . of intelligently directed configuration. It lets associated ontological and identity of design suspect chips lie where they fly.

    q: They are not material to the logic, apart from, we know designers are possible and that intelligence is a manifestation of rationality.

    r: Exploration of same, on other arguments and even disciplines, showing — whether or no you may like it — that we cannot bind intelligence to embodiment on computational substrates.

    s: In the case of the world of life, we see in the OP a demonstrated case of known intelligent design at genome scope, which is a breakthrough as — published in Nature — we have actual demonstration of intelligent design of a life form, so by Newton’s rules we have no good warrant to ideologically lock out the possibility of intelligently directed configuration of cell based life at origin or at origin of body plans.

    t: Where, repeat, there is no good reason to bind designing intelligence to embodiment on computational substrates, starting with sharply different characteristics,

    u: especially, that such substrates are inherently non-rational but rather are blindly mechanical and/or stochastic.

    >>and claim that it is independent of God.>>

    v: Yes, because it is an inductive inference on tested, reliable sign to credible causal PROCESS, not a speculative inference as to ontological character or identity of possible causal agents.

    w: That distinction must be preserved if there is to be a genuine understanding and responsible discussion. That too often, insistently (and in the face of cogent correction) such is not done, speaks volumes about the motivations of too many objectors to design.

    >> Do you have your cake and eat it much?>>

    x: This, instead only shows biased projections and a cluster of mutually reinforcing fallacies in action, as outlined.

    It is time for objectors to leave behind long since corrected fallacies amounting to a characteristic pattern of misleading argument: red herrings –> strawmen –> ad homs –> clouding, confusing, poisoning and polarising the atmosphere, frustrating serious discussion but reinforcing polarisation and unjustified ideological imposition of a priori evolutionary materialistic scientism, closing and clouding minds.

    KF

  254. 254
    hazel says:

    This is a new one: if person A makes an argument against person B, and person C agrees with A, person C is engaging in “piling-on”.

    We’ll have to add the “pile-on tactic” to our list of nefarious rhetorical and agit-prop behaviors, along with “red herrings –> strawmen –> ad homs –> clouding, confusing, poisoning and polarising the atmosphere, frustrating serious discussion but reinforcing polarisation and unjustified ideological imposition of a priori evolutionary materialistic scientism, closing and clouding minds.”

  255. 255
    Brother Brian says:

    KF@253, you sound like a man trying to convince himself of something.

    I admit that my inference is absurd. I juxtaposed it against the ID inference to demonstrated that it is even more absurd. The fact that you have gone to such lengths to try to deride my inference suggests that I have hit close to home.

  256. 256
    Ed George says:

    Hazel@254, I thought the response to a simple statement was a little over the top. But we all have bad days. And it appears that BB is giving KF one. 🙂

  257. 257
    kairosfocus says:

    H,

    piling on occurs when we see not cogent response but mere voting in support without addressing serious corrections to errors, especially when introduced by concern troll tactics.

    BB,

    There is a point by point corrective on the table, provide a cogent reply or it is clear that you do not have an answer, only a position.

    EG,

    You set off from the classic introduction of the concern troll, to pile on.

    >>>>>>>>>>>>>>

    None of the above is substantial, I hereby attach the above point by point corrective to show the current balance on merits:

    >>Let me address your latest claim in steps of thought:

    >>If I make an inference that all known designers are embodied beings>>

    a: Begs the question, billions for cause beg to differ.

    b: One cannot simply imply delusion on that scale, as it would undermine (self-referentially) the credibility of human rationality.

    c: In short, your first premise locks out any conclusion other than the one you wish and is dubious, highly debatable.

    d: Further to this, you have consistently failed to address the other design inference, fine tuning. This points to extra-cosmic designer.

    e: Yet further, the logic of being requires a finitely remote necessary being world root capable of causing a fine tuned C-Chem aqueous medium cell based life facilitating cosmos. Necessary beings cannot be composed of arranged, independently existing proper parts. That may be unfamiliar to you but is readily established as composite entities are inherently contingent.

    f: There is good reason to set aside your first premise and recognise instead that we observe designing intelligences so designing intelligence is possible. Without question-begging ontological commitments.

    >> therefore all designers are most likely embodied individuals,>>

    g: Reasoning on a begged question goes in pointless circles.

    h: Further, this side-steps the point I have elaborated above, on the known ideology at work across our civilisation, evolutionary materialistic scientism, i.e. you are setting up a strawman to knock over.

    i: On this ideology, intelligence is founded on sufficiently sophisticated computational substrates, but it is readily seen that these are blind, mechanically and/or stochastically governed glorified calculating engines, not responsibly and rationally free reasoning entities. Never mind pretentions of AI, they are inherently not freely thinking intelligences.

    j: Thus, it is an error to seek to bind intelligence to embodiment. Intelligences may indeed be embodied, but this points to an “amphibian” ontological character: mind over matter.

    k: I clip from above — which you ducked in order to revert to a compound fallacy now being answered point by point:

    What we actually observe is:

    A: [material computational substrates] –X –> [rational inference]

    B: [material computational substrates] —-> [mechanically and/or stochastically governed computation]

    C: [intelligent agents] —-> [rational, freely chosen, morally governed inference]

    D: [embodied intelligent agents] —-> [rational, freely chosen, morally governed inference]

    The set of observations A through D imply that intelligent agency transcends computation, as their characteristics and capabilities are not reducible to:

    – components and their device physics,
    – organisation as circuits and networks [e.g. gates, flip-flops, registers, operational amplifiers (especially integrators), ball-disk integrators, neuron-gates and networks, etc],
    – organisation/ architecture forming computational circuits, systems and cybernetic entities,
    – input signals,
    – stored information,
    – processing/algorithm execution,
    – outputs

    >> it is not valid because I haven’t taken God into account.>>

    l: Motive mongering, given widespread polarisation once “God” is mentioned.

    m: Above and previously, I have pointed out that billions will disagree, for cause, with the claim that ALL intelligences we have observed are embodied, i.e. I pointed to question-begging and further to the implications of implying such widespread delusion. Including, self-referential implications for you.

    n: Further, I have already taken much time and effort to mark the ontological differences between computational substrates and freely acting, insightful, morally governed intelligence. That counts and we scan above, in vain, for a cogent answer on your part.

    >> But ID can make a very similar inference>>

    o: You really need to read the UD weak argument correctives and take their points seriously, even if you disagree with our conclusions.

    p: The design inference is an inference on reliable signs, from observed functionally specific, sufficiently complex, configuration based organisation and associated information to a causal process . . . not agency . . . of intelligently directed configuration. It lets associated ontological and identity of design suspect chips lie where they fly.

    q: They are not material to the logic, apart from, we know designers are possible and that intelligence is a manifestation of rationality.

    r: Exploration of same, on other arguments and even disciplines, showing — whether or no you may like it — that we cannot bind intelligence to embodiment on computational substrates.

    s: In the case of the world of life, we see in the OP a demonstrated case of known intelligent design at genome scope, which is a breakthrough as — published in Nature — we have actual demonstration of intelligent design of a life form, so by Newton’s rules we have no good warrant to ideologically lock out the possibility of intelligently directed configuration of cell based life at origin or at origin of body plans.

    t: Where, repeat, there is no good reason to bind designing intelligence to embodiment on computational substrates, starting with sharply different characteristics,

    u: especially, that such substrates are inherently non-rational but rather are blindly mechanical and/or stochastic.

    >>and claim that it is independent of God.>>

    v: Yes, because it is an inductive inference on tested, reliable sign to credible causal PROCESS, not a speculative inference as to ontological character or identity of possible causal agents.

    w: That distinction must be preserved if there is to be a genuine understanding and responsible discussion. That too often, insistently (and in the face of cogent correction) such is not done, speaks volumes about the motivations of too many objectors to design.

    >> Do you have your cake and eat it much?>>

    x: This, instead only shows biased projections and a cluster of mutually reinforcing fallacies in action, as outlined. >>

    That is what needs to be answered, cogently.

    KF

    KF

  258. 258
    Brother Brian says:

    I seem to remember a debating strategy that involves focusing on overwhelming an opponent with as many arguments as possible, without regard for accuracy or strength of the arguments. I can’t remember what it is called. But I think we are seeing a prime example of this. Although, I am surprised that KF didn’t have points for the last two letters of the alphabet.

  259. 259
    daveS says:

    KF,

    … speaks volumes about the motivations of too many objectors to design.

    In the same post where you complain about motive mongering on the part of your interlocutors.

    Let’s be honest—you are responsible for more red herrings, strawmen, and motive mongering than all of us combined.

  260. 260
    hazel says:

    Piling on: Yes to 258 and 259.

  261. 261
    kairosfocus says:

    BB, wrong again, and insubstantial. If I interact with you and respond, you object insubstantially. If I take you up point bu point the same, it is obvious you have no intent to address the substantial matters. That leaves the balance on merits clear, and not in your favour. KF

    PS: For record, I again show what you need to answer cogently and this is not a mere flood of empty words, it is speaking to substance:

    >>>>>>>>>>
    I hereby attach the above point by point corrective to show the current balance on merits:

    >>Let me address your latest claim in steps of thought:

    >>If I make an inference that all known designers are embodied beings>>

    a: Begs the question, billions for cause beg to differ.

    b: One cannot simply imply delusion on that scale, as it would undermine (self-referentially) the credibility of human rationality.

    c: In short, your first premise locks out any conclusion other than the one you wish and is dubious, highly debatable.

    d: Further to this, you have consistently failed to address the other design inference, fine tuning. This points to extra-cosmic designer.

    e: Yet further, the logic of being requires a finitely remote necessary being world root capable of causing a fine tuned C-Chem aqueous medium cell based life facilitating cosmos. Necessary beings cannot be composed of arranged, independently existing proper parts. That may be unfamiliar to you but is readily established as composite entities are inherently contingent.

    f: There is good reason to set aside your first premise and recognise instead that we observe designing intelligences so designing intelligence is possible. Without question-begging ontological commitments.

    >> therefore all designers are most likely embodied individuals,>>

    g: Reasoning on a begged question goes in pointless circles.

    h: Further, this side-steps the point I have elaborated above, on the known ideology at work across our civilisation, evolutionary materialistic scientism, i.e. you are setting up a strawman to knock over.

    i: On this ideology, intelligence is founded on sufficiently sophisticated computational substrates, but it is readily seen that these are blind, mechanically and/or stochastically governed glorified calculating engines, not responsibly and rationally free reasoning entities. Never mind pretentions of AI, they are inherently not freely thinking intelligences.

    j: Thus, it is an error to seek to bind intelligence to embodiment. Intelligences may indeed be embodied, but this points to an “amphibian” ontological character: mind over matter.

    k: I clip from above — which you ducked in order to revert to a compound fallacy now being answered point by point:

    What we actually observe is:

    A: [material computational substrates] –X –> [rational inference]

    B: [material computational substrates] —-> [mechanically and/or stochastically governed computation]

    C: [intelligent agents] —-> [rational, freely chosen, morally governed inference]

    D: [embodied intelligent agents] —-> [rational, freely chosen, morally governed inference]

    The set of observations A through D imply that intelligent agency transcends computation, as their characteristics and capabilities are not reducible to:

    – components and their device physics,
    – organisation as circuits and networks [e.g. gates, flip-flops, registers, operational amplifiers (especially integrators), ball-disk integrators, neuron-gates and networks, etc],
    – organisation/ architecture forming computational circuits, systems and cybernetic entities,
    – input signals,
    – stored information,
    – processing/algorithm execution,
    – outputs

    >> it is not valid because I haven’t taken God into account.>>

    l: Motive mongering, given widespread polarisation once “God” is mentioned.

    m: Above and previously, I have pointed out that billions will disagree, for cause, with the claim that ALL intelligences we have observed are embodied, i.e. I pointed to question-begging and further to the implications of implying such widespread delusion. Including, self-referential implications for you.

    n: Further, I have already taken much time and effort to mark the ontological differences between computational substrates and freely acting, insightful, morally governed intelligence. That counts and we scan above, in vain, for a cogent answer on your part.

    >> But ID can make a very similar inference>>

    o: You really need to read the UD weak argument correctives and take their points seriously, even if you disagree with our conclusions.

    p: The design inference is an inference on reliable signs, from observed functionally specific, sufficiently complex, configuration based organisation and associated information to a causal process . . . not agency . . . of intelligently directed configuration. It lets associated ontological and identity of design suspect chips lie where they fly.

    q: They are not material to the logic, apart from, we know designers are possible and that intelligence is a manifestation of rationality.

    r: Exploration of same, on other arguments and even disciplines, showing — whether or no you may like it — that we cannot bind intelligence to embodiment on computational substrates.

    s: In the case of the world of life, we see in the OP a demonstrated case of known intelligent design at genome scope, which is a breakthrough as — published in Nature — we have actual demonstration of intelligent design of a life form, so by Newton’s rules we have no good warrant to ideologically lock out the possibility of intelligently directed configuration of cell based life at origin or at origin of body plans.

    t: Where, repeat, there is no good reason to bind designing intelligence to embodiment on computational substrates, starting with sharply different characteristics,

    u: especially, that such substrates are inherently non-rational but rather are blindly mechanical and/or stochastic.

    >>and claim that it is independent of God.>>

    v: Yes, because it is an inductive inference on tested, reliable sign to credible causal PROCESS, not a speculative inference as to ontological character or identity of possible causal agents.

    w: That distinction must be preserved if there is to be a genuine understanding and responsible discussion. That too often, insistently (and in the face of cogent correction) such is not done, speaks volumes about the motivations of too many objectors to design.

    >> Do you have your cake and eat it much?>>

    x: This, instead only shows biased projections and a cluster of mutually reinforcing fallacies in action, as outlined. >>

    That is what needs to be answered, cogently.

  262. 262
    hazel says:

    For the record, kf, you have now posted the same thing three times in a row, for the record. That’s seems like a redundant record to me.

  263. 263
    hazel says:

    Let’s just take one point: BB says, “If I make an inference that all known designers are embodied beings,”, you replied, above, “Millions of people personally know God in positively life-transforming ways, for example.”

    It is hard for me to take people’s religious experiences of God as empirically similar in any way to the fact that we can watch people design and build things. It’s hard to dig in “cogently” to all your other points if that’s where you start.

    Are we still talking science here?

  264. 264
    Brother Brian says:

    Hazel

    Are we still talking science here?

    Of course not. We are talking ID. 🙂

  265. 265
    kairosfocus says:

    H, you have at least begun to respond. I suggest there are life transforming encounters with God that are the experience and understanding of many millions. This includes miracles of several sorts. For me, it specifically includes why I am not 50 years since, dead. There are many more, and experience of God or the good is not the only category of cases. My point is, that there is far more to the world of credible experience and observation than BB would allow, and that if all of this is swept away, it raises the spectre of grand delusion, thus self referential undermining of rationality. KF

  266. 266
    kairosfocus says:

    BB, your prejudices, impositions and question beggings are showing. On the specifically scientific, I have pointed to something I intimately know: the characteristics of computational substrates vs attributes required for intelligence, leading to distinct identity that breaks attempts to bind the latter to the former, undermining your attempted induction as a post hoc fallacy. Going beyond, I have also pointed to fine tuning as a domain pointing to a cosmological act of design, directly implying designer antecedent to a world of atomic or similar matter and thus also extracosmic. I note also your continued resort to loaded talking points while failing to address the substantial matter cogently. KF

  267. 267
    Brother Brian says:

    KF@266, what does computational substrates have to do with anything? It is completely irrelevant to whether or not my inference is less absurd that the ID inference. My inference accepts the possibility of life being designed, but infers, on cause, that the designer is most likely embodied.

    And fine tuning is a farce. To make the argument that what you are calling fine tuning was the result of an extra cosmic intelligence, you first have to demonstrate that other physical constants are possible. Just because something is impossible doesn’t mean that it is designed. A rock will always sink in a lake at room temperature. That doesn’t mean the rock is designed.

    The alphabet soup of “arguments” you keep posting do nothing to change any of this.

  268. 268
    hazel says:

    kf, the point of the OP (remember the OP?) was that human beings (material designers), working within a context of an existing genetic code, made changes that served as support for ID. How do religious experiences of God relate to this argument? This seems, dare I say, a big tangent and a significant distraction.

  269. 269
    Brother Brian says:

    Hazel

    This seems, dare I say, a big tangent and a significant distraction.

    To say the least. Where’s my use of the inference was right on topic.

  270. 270
    kairosfocus says:

    BB (& attn H), you full well know that a wetware, computational substrate, the brain, is held to be the seat of intelligence by the institutionally dominant (but self-refuting) evolutionary materialist school of thought. Only, it is easy to show that such a substrate is inherently non-rational, so this fails. Similarly, the strong AI dream hopes that a combination of software, orgamisation and an underlying substrate will adequately show itself intelligent — only to repeatedly fail. Likewise, the so-called hard problem of consciousness is held to be about how consciousness and its key characteristics somehow emerge from brain structures and activity, which again faces the problem that even refined and highly organised rock forming wetware inherently is a computational substrate with all the limitations of such. So, attempts to bind intelligence to embodiment are implicitly about this failed materialistic dream. The rhetorical pretence that it is irrelevant to point out the inherent non-rationality of computational substrates, fails. There is simply no “simple”, non- question begging, non ideologically loaded inference from the fact that some people point to embodied intelligent creatures, dismiss the experiences and views of a very large fraction of humanity that they have experience also of non-embodied intelligence, refuse to attend to evidence of the categorical difference between computation and rational inference (which raises the “mind over matter” question that we could instead be exploring via the Smith Model, etc), and the claimed conclusion that it is likely or definitive that all relevant intelligences are similarly embodied. KF

    PS: Again, Reppert:

    . . . let us suppose that brain state A [–> notice, state of a wetware, electrochemically operated computational substrate], which is token identical to the thought that all men are mortal, and brain state B, which is token identical to the thought that Socrates is a man, together cause the belief [–> concious, perceptual state or disposition] that Socrates is mortal. It isn’t enough for rational inference that these events be those beliefs, it is also necessary that the causal transaction be in virtue of the content of those thoughts . . . [But] if naturalism is true, then the propositional content is irrelevant to the causal transaction that produces the conclusion, and [so] we do not have a case of rational inference. In rational inference, as Lewis puts it, one thought causes another thought not by being, but by being seen to be, the ground for it. But causal transactions in the brain occur in virtue of the brain’s being in a particular type of state that is relevant to physical causal transactions.

  271. 271
    kairosfocus says:

    F/N: I think it is relevant to expand, by excerpting the current form of my longstanding discussion of the minds are evolved brains in a materialistic world thesis, and why it is self-referential, incoherent and necessarily false. Never mind the lab coat it may wear, or its claim to be a simple inductive inference from what we readily see:

    First, some materialists actually suggest that mind is more or less a delusion, which is instantly self-referentially absurd. For instance, Sir Francis Crick is on record, in his 1994 The Astonishing Hypothesis:

    . . . that “You”, your joys and your sorrows, your memories and your ambitions, your sense of personal identity and free will, are in fact no more than the behaviour of a vast assembly of nerve cells and their associated molecules. As Lewis Carroll’s Alice might have phrased: “You’re nothing but a pack of neurons.” This hypothesis is so alien to the ideas of most people today that it can truly be called astonishing.

    Philip Johnson has replied that Sir Francis should have therefore been willing to preface his works thusly: “I, Francis Crick, my opinions and my science, and even the thoughts expressed in this book, consist of nothing more than the behavior of a vast assembly of nerve cells and their associated molecules.” Johnson then acidly commented: “[t]he plausibility of materialistic determinism requires that an implicit exception be made for the theorist.” [Reason in the Balance, 1995.]

    In short, it is at least arguable that self-referential absurdity is the dagger pointing to the heart of evolutionary materialistic models of mind and its origin. For, there is a very good reason we are cautioned about how easily self-referential statements can become self-refuting, like a snake attacking and swallowing itself tail-first. Any human scheme of thought that undermines responsible [thus, morally governed] rational freedom undermines itself fatally. We thus see inadvertent, inherent self-falsification of evolutionary materialism. But, “inadvertent” counts: it can be hard to recognise and acknowledge the logically fatal nature of the result. Of course, that subjective challenge does not change the objective result: self-referential incoherence and irretrievable self-falsification. (An audio clip, here, by William Lane Craig that summarises Plantinga’s argument on this in a nutshell, is useful as a quick reference.)

    This issue can be discussed at a much higher level, but it can also be drawn out a bit in a fairly simple way for blog level discussion:

    a: Evolutionary materialism argues that the cosmos is the product of chance interactions of matter and energy, within the constraint of the laws of nature; from hydrogen to humans by undirected chance and necessity.

    b: Therefore, all phenomena in the universe, without residue, are determined by the working of purposeless laws of chance and/or mechanical necessity acting on material objects, under the direct or indirect control of happenstance initial circumstances.

    (This is physicalism. This view covers both the forms where (a) the mind and the brain are seen as one and the same thing, and those where (b) somehow mind emerges from and/or “supervenes” on brain, perhaps as a result of sophisticated and complex software looping. The key point, though is as already noted: physical causal closure — the phenomena that play out across time, without residue, are in principle deducible or at least explainable up to various random statistical distributions and/or mechanical laws, from prior physical states. Such physical causal closure, clearly, implicitly discounts or even dismisses the causal effect of concept formation and reasoning then responsibly deciding, in favour of specifically physical interactions in the brain-body control loop; indeed, some mock the idea of — in their view — an “obviously” imaginary “ghost” in the meat-machine. [There is also some evidence from simulation exercises, that accuracy of even sensory perceptions may lose out to utilitarian but inaccurate ones in an evolutionary competition. “It works” does not warrant the inference to “it is true.”] )

    c: But human thought, clearly a phenomenon in the universe, must now fit into this meat-machine picture. So, we rapidly arrive at Crick’s claim in his The Astonishing Hypothesis (1994): what we subjectively experience as “thoughts,” “reasoning” and “conclusions” can only be understood materialistically as the unintended by-products of the blind natural forces which cause and control the electro-chemical events going on in neural networks in our brains that (as the Smith Model illustrates) serve as cybernetic controllers for our bodies.

    d: These underlying driving forces are viewed as being ultimately physical, but are taken to be partly mediated through a complex pattern of genetic inheritance shaped by forces of selection [“nature”] and psycho-social conditioning [“nurture”], within the framework of human culture [i.e. socio-cultural conditioning and resulting/associated relativism]. And, remember, the focal issue to such minds — notice, this is a conceptual analysis made and believed by the materialists! — is the physical causal chains in a control loop, not the internalised “mouth-noises” that may somehow sit on them and come along for the ride.

    (Save, insofar as such “mouth noises” somehow associate with or become embedded as physically instantiated signals or maybe codes in such a loop. [How signals, languages and codes originate and function in systems in our observation of such origin — i.e by design — tends to be pushed to the back-burner and conveniently forgotten. So does the point that a signal or code takes its significance precisely from being an intelligently focused on, observed or chosen and significant alternative from a range of possibilities that then can guide decisive action.])

    e: For instance, Marxists commonly derided opponents for their “bourgeois class conditioning” — but what of the effect of their own class origins? Freudians frequently dismissed qualms about their loosening of moral restraints by alluding to the impact of strict potty training on their “up-tight” critics — but doesn’t this cut both ways? Should we not ask a Behaviourist whether s/he is little more than yet another operantly conditioned rat trapped in the cosmic maze? And — as we saw above — would the writings of a Crick be any more than the firing of neurons in networks in his own brain?

    f: For further instance, we may take the favourite whipping-boy of materialists: religion. Notoriously, they often hold that belief in God is not merely cognitive, conceptual error, but delusion. Borderline lunacy, in short. But, if such a patent “delusion” is so utterly widespread, even among the highly educated, then it “must” — by the principles of evolution — somehow be adaptive to survival, whether in nature or in society. And so, this would be a major illustration of the unreliability of our conceptual reasoning ability, on the assumption of evolutionary materialism.

    g: Turning the materialist dismissal of theism around, evolutionary materialism itself would be in the same leaky boat. For, the sauce for the goose is notoriously just as good a sauce for the gander, too.

    h: That is, on its own premises [and following Dawkins in A Devil’s Chaplain, 2004, p. 46], the cause of the belief system of evolutionary materialism, “must” also be reducible to forces of blind chance and mechanical necessity that are sufficiently adaptive to spread this “meme” in populations of jumped- up apes from the savannahs of East Africa scrambling for survival in a Malthusian world of struggle for existence. Reppert brings the underlying point sharply home, in commenting on the “internalised mouth-noise signals riding on the physical cause-effect chain in a cybernetic loop” view:

    . . . let us suppose that brain state A [–> notice, state of a wetware, electrochemically operated computational substrate], which is token identical to the thought that all men are mortal, and brain state B, which is token identical to the thought that Socrates is a man, together cause the belief [–> concious, perceptual state or disposition] that Socrates is mortal. It isn’t enough for rational inference that these events be those beliefs, it is also necessary that the causal transaction be in virtue of the content of those thoughts . . . [But] if naturalism is true, then the propositional content is irrelevant to the causal transaction that produces the conclusion, and [so] we do not have a case of rational inference. In rational inference, as Lewis puts it, one thought causes another thought not by being, but by being seen to be, the ground for it. But causal transactions in the brain occur in virtue of the brain’s being in a particular type of state that is relevant to physical causal transactions.

    i: The famous geneticist and evolutionary biologist (as well as Socialist) J. B. S. Haldane made much the same point in a famous 1932 remark:

    “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. 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. (NB: DI Fellow, Nancy Pearcey brings this right up to date (HT: ENV) in a current book, Finding Truth.)]

    j: Therefore, though materialists will often try to pointedly ignore or angrily brush aside the issue, we may freely argue: if such evolutionary materialism is true, then (i) our consciousness, (ii) the “thoughts” we have, (iii) the conceptualised beliefs we hold, (iv) the reasonings we attempt based on such and (v) the “conclusions” and “choices” (a.k.a. “decisions”) we reach — without residue — must be produced and controlled by blind forces of chance happenstance and mechanical necessity that are irrelevant to “mere” ill-defined abstractions such as: purpose or truth, or even logical validity.

    (NB: The conclusions of such “arguments” may still happen to be true, by astonishingly lucky coincidence — but we have no rational grounds for relying on the “reasoning” that has led us to feel that we have “proved” or “warranted” them. It seems that rationality itself has thus been undermined fatally on evolutionary materialistic premises. Including that of Crick et al. Through, self-reference leading to incoherence and utter inability to provide a cogent explanation of our commonplace, first-person experience of reasoning and rational warrant for beliefs, conclusions and chosen paths of action. Reduction to absurdity and explanatory failure in short.)

    k: And, if materialists then object: “But, we can always apply scientific tests, through observation, experiment and measurement,” then we must immediately note that — as the fate of Newtonian Dynamics between 1880 and 1930 shows — empirical support is not equivalent to establishing the truth of a scientific theory. For, at any time, one newly discovered countering fact can in principle overturn the hitherto most reliable of theories. (And as well, we must not lose sight of this: in science, one is relying on the legitimacy of the reasoning process to make the case that scientific evidence provides reasonable albeit provisional warrant for one’s beliefs etc. Scientific reasoning is not independent of reasoning.)

    l: Worse, in the case of origins science theories, we simply were not there to directly observe the facts of the remote past, so origins sciences are even more strongly controlled by assumptions and inferences than are operational scientific theories. So, we contrast the way that direct observations of falling apples and orbiting planets allow us to test our theories of gravity.

    m: Moreover, as Harvard biologist Richard Lewontin reminds us all in his infamous January 29, 1997 New York Review of Books article, “Billions and billions of demons,” it is now notorious that:

    . . . It is not that the methods and institutions of science somehow compel [[materialistic scientists] to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. [And if you have been led to imagine that the immediately following words justify the above, kindly cf. the more complete clip and notes here.]

    n: Such a priori assumptions of materialism are patently question-begging, mind-closing and fallacious.

    o: More important, to demonstrate that empirical tests provide empirical support to the materialists’ theories would require the use of the very process of reasoning and inference which they have discredited.

    p: Thus, evolutionary materialism arguably reduces reason itself to the status of illusion. But, as we have seen: immediately, that must include “Materialism.”

    q: In the end, it is thus quite hard to escape the conclusion that materialism is based on self-defeating, question-begging logic.

    r: So, while materialists — just like the rest of us — in practice routinely rely on the credibility of reasoning and despite all the confidence they may project, they at best struggle to warrant such a tacitly accepted credibility of mind and of concepts and reasoned out conclusions relative to the core claims of their worldview. (And, sadly: too often, they tend to pointedly ignore or rhetorically brush aside the issue.)

    KF

  272. 272
    Brother Brian says:

    KF

    BB (& attn H), you full well know that a wetware, computational substrate, the brain, is held to be the seat of intelligence by the institutionally dominant (but self-refuting) evolutionary materialist school of thought.

    How is that in any way relevant to the validity of my inference? ID has never excluded an embodied designer as being responsible for life on earth. My inference, following the same logic as the ID inference, just shows that an embodied designer is the best explanation for life.

  273. 273
    kairosfocus says:

    BB, your appeal above to the Gish-memory slander [he is not alive to point out that he won hundreds of public debates on the merits of the systematic gaps in the fossil record, the trade secret of paleontology] even while ducking answering the substantial reasons I have given why your claimed simple inference subverts the force of the OP only serve to show that a serious question on the table at this point is whether you are simply manifesting trollish willful obtuseness and a veritable zoo of other fallacies. If the response I have made to why attempts to bind intelligence to embodiment are so weak, then show that by cogent, substantial argument or stand exposed as using dismissive talking points to evade the force of a refutation and correction of a cluster of errors. KF

    PS: As this is a point by point response to your specific claims, I again lay out for record, noting that the following should be understood in context of the thread above:

    [BB:]>>If I make an inference that all known designers are embodied beings>>

    a: Begs the question, billions for cause beg to differ.

    b: One cannot simply imply delusion on that scale, as it would undermine (self-referentially) the credibility of human rationality.

    c: In short, your first premise locks out any conclusion other than the one you wish and is dubious, highly debatable.

    d: Further to this, you have consistently failed to address the other design inference, fine tuning. This points to extra-cosmic designer.

    e: Yet further, the logic of being requires a finitely remote necessary being world root capable of causing a fine tuned C-Chem aqueous medium cell based life facilitating cosmos. Necessary beings cannot be composed of arranged, independently existing proper parts. That may be unfamiliar to you but is readily established as composite entities are inherently contingent.

    f: There is good reason to set aside your first premise and recognise instead that we observe designing intelligences so designing intelligence is possible. Without question-begging ontological commitments.

    >> therefore all designers are most likely embodied individuals,>>

    g: Reasoning on a begged question goes in pointless circles.

    h: Further, this side-steps the point I have elaborated above, on the known ideology at work across our civilisation, evolutionary materialistic scientism, i.e. you are setting up a strawman to knock over.

    i: On this ideology, intelligence is founded on sufficiently sophisticated computational substrates, but it is readily seen that these are blind, mechanically and/or stochastically governed glorified calculating engines, not responsibly and rationally free reasoning entities. Never mind pretentions of AI, they are inherently not freely thinking intelligences.

    j: Thus, it is an error to seek to bind intelligence to embodiment. Intelligences may indeed be embodied, but this points to an “amphibian” ontological character: mind over matter.

    k: I clip from above — which you ducked in order to revert to a compound fallacy now being answered point by point:

    What we actually observe is:

    A: [material computational substrates] –X –> [rational inference]

    B: [material computational substrates] —-> [mechanically and/or stochastically governed computation]

    C: [intelligent agents] —-> [rational, freely chosen, morally governed inference]

    D: [embodied intelligent agents] —-> [rational, freely chosen, morally governed inference]

    The set of observations A through D imply that intelligent agency transcends computation, as their characteristics and capabilities are not reducible to:

    – components and their device physics,
    – organisation as circuits and networks [e.g. gates, flip-flops, registers, operational amplifiers (especially integrators), ball-disk integrators, neuron-gates and networks, etc],
    – organisation/ architecture forming computational circuits, systems and cybernetic entities,
    – input signals,
    – stored information,
    – processing/algorithm execution,
    – outputs

    >> it is not valid because I haven’t taken God into account.>>

    l: Motive mongering, given widespread polarisation once “God” is mentioned.

    m: Above and previously, I have pointed out that billions will disagree, for cause, with the claim that ALL intelligences we have observed are embodied, i.e. I pointed to question-begging and further to the implications of implying such widespread delusion. Including, self-referential implications for you.

    n: Further, I have already taken much time and effort to mark the ontological differences between computational substrates and freely acting, insightful, morally governed intelligence. That counts and we scan above, in vain, for a cogent answer on your part.

    >> But ID can make a very similar inference>>

    o: You really need to read the UD weak argument correctives and take their points seriously, even if you disagree with our conclusions.

    p: The design inference is an inference on reliable signs, from observed functionally specific, sufficiently complex, configuration based organisation and associated information to a causal process . . . not agency . . . of intelligently directed configuration. It lets associated ontological and identity of design suspect chips lie where they fly.

    q: They are not material to the logic, apart from, we know designers are possible and that intelligence is a manifestation of rationality.

    r: Exploration of same, on other arguments and even disciplines, showing — whether or no you may like it — that we cannot bind intelligence to embodiment on computational substrates.

    s: In the case of the world of life, we see in the OP a demonstrated case of known intelligent design at genome scope, which is a breakthrough as — published in Nature — we have actual demonstration of intelligent design of a life form, so by Newton’s rules we have no good warrant to ideologically lock out the possibility of intelligently directed configuration of cell based life at origin or at origin of body plans.

    t: Where, repeat, there is no good reason to bind designing intelligence to embodiment on computational substrates, starting with sharply different characteristics,

    u: especially, that such substrates are inherently non-rational but rather are blindly mechanical and/or stochastic.

    >>and claim that it is independent of God.>>

    v: Yes, because it is an inductive inference on tested, reliable sign to credible causal PROCESS, not a speculative inference as to ontological character or identity of possible causal agents.

    w: That distinction must be preserved if there is to be a genuine understanding and responsible discussion. That too often, insistently (and in the face of cogent correction) such is not done, speaks volumes about the motivations of too many objectors to design.

    >> Do you have your cake and eat it much?>>

    x: This, instead only shows biased projections and a cluster of mutually reinforcing fallacies in action, as outlined.>>

  274. 274
    kairosfocus says:

    BB, at this point, it is quite evident that you imagine that by pretending to have made a simple, non question begging, non ideologically loaded inference, you can dismiss or at least distract attention from what was definitively shown in the OP. I have taken time to show, step by step and by interaction and explanation why the claimed simple inductive inference, once it is seen in context of the state of thought on brains, minds and the like, fails. That you complain and suggest invidious associations with a longstanding smear against a man who won hundreds of open debates on the merits rather than answer on the merits in the end tells us that you do not have a cogent, substantial case but rely on the force of the dominance of evolutionary materialist indoctrination to project a sense of plausibility. Fail, in short. KF

  275. 275
    kairosfocus says:

    F/N: I have added a PPPS to the OP which provides a context in brief, an audio clip on evolutionary materialist undermining of the credibility of the rationality of mind, a look at the Smith, two-tier controller bio-cybernetic model, and Reppert’s telling summary in brief on why computational substrates fail to credibly account for rational inference, thus wider rational thought. KF

  276. 276
    Brother Brian says:

    KF, I am finding it really hard to follow your logic. On one hand you are saying that it is essentially impossible for the designer of life to be an embodied being, and on the other hand you are claiming that the paper describing the synthesis of a genome by an embodied being is a breakthrough for ID.

  277. 277
    kairosfocus says:

    H,

    Let’s take up your remarks in steps of thought:

    >> the point of the OP (remember the OP?) was that human beings (material designers),>>

    a: See the ideologically loaded, question-begging inference that human beings are material as opposed to embodied entities?

    b: This already demonstrates why it is relevant to show that the presumed seat of material intelligence and thus of intelligently directed configuration (design) is the brain, a computational substrate, which is subject to the limitations of such substrates.

    c: Let me presume you can readily see Reppert’s compressed summary and point to Haldane in a similar vein, he who was a co-founder of the neo-darwinist synthesis:

    “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. 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. (NB: DI Fellow, Nancy Pearcey brings this right up to date (HT: ENV) in a current book, Finding Truth.)]

    c: The case is already made in a nutshell, but I will note: many observed designers are indeed embodied but we have no good warrant for inferring to embodiment and associated computational substrates are the warranted, credible seat and source of intelligence and rationality.

    >>working within a context of an existing genetic code, made changes that served as support for ID.>>

    d: Yes, the designers definitively showed and published in Nature, that a molecular nanotech lab can design and synthesise a whole genome, insert same in a cell body and get it to work.

    e: What this warrants is the recognition that intelligent design of cell based life using molecular nanotech techniques is possible, so intelligent design of life and of life forms is possible, as manifestly actual in our observation.

    f: Further to this, there is now no further defence of ideological lockouts of the possibility of such design in the remote past of origins, so ID cannot be properly locked out.

    g: This then immediately leads to the Brexit Party phenomenon. Once admitted, instantly the strong horse. Especially as there is no actually observed empirical warrant that blind chance and/or mechanical necessity can and does create and organise similarly complex molecular nanotech. For details cf Tour’s vid.

    h: However, this by no means establishes that the only possible or plausible seat of designing intelligence is embodiment with computational substrates as key locus. Instead, we see an identity-defining characteristics/properties categorical distinction, as:

    What we actually observe is:

    A: [material computational substrates] –X –> [rational inference]

    B: [material computational substrates] —-> [mechanically and/or stochastically governed computation]

    C: [intelligent agents] —-> [rational, freely chosen, morally governed inference]

    D: [embodied intelligent agents] —-> [rational, freely chosen, morally governed inference]

    The set of observations A through D imply that intelligent agency transcends computation, as their characteristics and capabilities are not reducible to:

    – components and their device physics,
    – organisation as circuits and networks [e.g. gates, flip-flops, registers, operational amplifiers (especially integrators), ball-disk integrators, neuron-gates and networks, etc],
    – organisation/ architecture forming computational circuits, systems and cybernetic entities,
    – input signals,
    – stored information,
    – processing/algorithm execution,
    – outputs

    >> How do religious experiences of God relate to this argument?>>

    i: Do you note your distancing and tainting labels? RELIGIOUS EXPERIENCES?

    j: No, we have experiences and observations of a large number of people that lead them to the conclusion that there are intelligent agents which are not embodied (some of these being life-transforming and rooted in miracles beyond the ordinary course of the natural world).

    k: These are so pervasive and so abundant that to write them all off as suspect or delusional is not merely to be duly skeptical of the suspect other; it would bring into question the rational credibility of the human mind. As I clipped above:

    e: For instance, Marxists commonly derided opponents for their “bourgeois class conditioning” — but what of the effect of their own class origins? Freudians frequently dismissed qualms about their loosening of moral restraints by alluding to the impact of strict potty training on their “up-tight” critics — but doesn’t this cut both ways? Should we not ask a Behaviourist whether s/he is little more than yet another operantly conditioned rat trapped in the cosmic maze? And — as we saw above — would the writings of a Crick be any more than the firing of neurons in networks in his own brain?

    f: For further instance, we may take the favourite whipping-boy of materialists: religion. Notoriously, they often hold that belief in God is not merely cognitive, conceptual error, but delusion. Borderline lunacy, in short. But, if such a patent “delusion” is so utterly widespread, even among the highly educated, then it “must” — by the principles of evolution — somehow be adaptive to survival, whether in nature or in society. And so, this would be a major illustration of the unreliability of our conceptual reasoning ability, on the assumption of evolutionary materialism.

    g: Turning the materialist dismissal of theism around, evolutionary materialism itself would be in the same leaky boat. For, the sauce for the goose is notoriously just as good a sauce for the gander, too.

    h: That is, on its own premises [and following Dawkins in A Devil’s Chaplain, 2004, p. 46], the cause of the belief system of evolutionary materialism, “must” also be reducible to forces of blind chance and mechanical necessity that are sufficiently adaptive to spread this “meme” in populations of jumped- up apes from the savannahs of East Africa scrambling for survival in a Malthusian world of struggle for existence . . .

    l: So, there is no non-question-begging warrant for the asserted claim, “all known designers are embodied beings.” All else inferred from that collapses into the fallacy of question-begging.

    m: Further to this, as was already pointed out in this comment, on distinct identity, we are better advised to conceive of ourselves as embodied intelligences, rather than implicitly conceding the notion that our conscious, rational intelligence has been explained on an electrochemical, wetware computational substrate.

    n: Going yet further, for rationality to be credible it must be free, not mechanically and/or stochastically driven and controlled without residue. Instead, it is morally governed through known — but evadable — duties to truth, right reason, prudence, warrant, fairness, justice etc.

    o: Thus, it stands on both sides of the IS-OUGHT gap, which can only be bridged at world-root level; pointing to a necessary (so, non-contingent, independent of external enabling causes and without beginning or end . . . aka eternal) being as world-source, where such a being is also inherently good.

    p: Further, the fine tuning of the observed cosmos points to an extra cosmic designer antecedent to atomic and related matter and energy.

    q: So, on many grounds, the imposition of embodiment is question-begging.

    >> This seems, dare I say, a big tangent and a significant distraction.>>

    r: I agree, that is why I find BB’s raising the claim, use of imposed ideological question begging, evasiveness on substance and repeated resort to dismissive talking points are at best a distraction.

    s: But, that having been put on the table as an intended counter-argument, it has to be substantially addressed, never mind the rhetorical pretence that the context for the question begging claim is not what it manifestly is.

    t: Further, such being the sorts of objections being raised, there is an underlying warrant to hold that the OP is being distracted from because its point is inconveniently well warranted.

    KF

  278. 278
    kairosfocus says:

    BB, you have yet again mischaracterised what I have said, not to mention the design inference and what design theory is about. I suggest you read my response to H just above and go on to read the UD weak argument correctives and take them to heart. Far too much of the institutionalised objections to ID turn on willful, correction-resisting mischaracterisation. Wiki being Exhibit A. I suggest, you mat find it useful to read the NWE presentation on ID by way of a third witness. KF

    PS: I add, the NWE intro-summ on ID:

    Intelligent design (ID) is the view that it is possible to infer from empirical evidence that “certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection” [1] Intelligent design cannot be inferred from complexity alone, since complex patterns often happen by chance. ID focuses on just those sorts of complex patterns that in human experience are produced by a mind that conceives and executes a plan. According to adherents, intelligent design can be detected in the natural laws and structure of the cosmos; it also can be detected in at least some features of living things.

    Greater clarity on the topic may be gained from a discussion of what ID is not considered to be by its leading theorists. Intelligent design generally is not defined the same as creationism, with proponents maintaining that ID relies on scientific evidence rather than on Scripture or religious doctrines. ID makes no claims about biblical chronology, and technically a person does not have to believe in God to infer intelligent design in nature. As a theory, ID also does not specify the identity or nature of the designer, so it is not the same as natural theology, which reasons from nature to the existence and attributes of God. ID does not claim that all species of living things were created in their present forms, and it does not claim to provide a complete account of the history of the universe or of living things.

    ID also is not considered by its theorists to be an “argument from ignorance”; that is, intelligent design is not to be inferred simply on the basis that the cause of something is unknown (any more than a person accused of willful intent can be convicted without evidence). According to various adherents, ID does not claim that design must be optimal; something may be intelligently designed even if it is flawed (as are many objects made by humans).

    Contents
    [hide]

    1 History
    2 Ideas of Some Leading ID Theorists
    2.1 Michael J. Behe
    2.2 William A. Dembski
    2.3 Stephen C. Meyer
    2.4 Guillermo Gonzalez and Jay W. Richards
    3 Some Aspects of the Controversy
    3.1 Philosophy
    3.2 Science
    3.3 Education
    3.4 Theology
    4 Notes and references
    5 Selected Bibliography
    5.1 Pro-ID Books
    5.2 Anti-ID Books
    6 External links
    6.1 Pro-ID Internet Sites
    6.2 Anti-ID Internet Sites
    7 Credits

    ID may be considered to consist only of the minimal assertion that it is possible to infer from empirical evidence that some features of the natural world are best explained by an intelligent agent. It conflicts with views claiming that there is no real design in the cosmos (e.g., materialistic philosophy) or in living things (e.g., Darwinian evolution) or that design, though real, is undetectable (e.g., some forms of theistic evolution). Because of such conflicts, ID has generated considerable controversy.

  279. 279
    kairosfocus says:

    BB,

    Perhaps against better judgement that on track record you will simply ignore a point by point substantial reply and continue to double down, I again take up your argument in corrective steps of thought:

    BB: >>I am finding it really hard to follow your logic.>>

    a: Q: Have you shown that by responding point by point, substantially? A: No.

    >>On one hand you are saying that it is essentially impossible for the designer of life to be an embodied being,>>

    b: At least you now use embodied, but conflate that with, necessarily, entirely material with intelligence traceable to the wetware computational substrate known as the brain.

    c: As you patently have not clicked and looked elsewhere or pondered the verbal summary of the Smith Model, I have placed it in a PPPS to the OP, showing the two-tier controller. There is already a linked discussion.

    d: The two-tier controller allows in-the-loop I/O control action AND beyond the loop supervision. Thus, embodied does not require locking in the evolutionary materialist, self-contradictory narrative on intelligence, its seat and cause.

    e: Therefore, I may freely look at embodied designers as designers without committing myself to any ontology of intelligence and its seat. That means, I am not forced to infer onward that the only warranted types of designers are embodied.

    f: where, much has already been put on the table regarding the categorical difference between computational substrates and their characteristics on one hand, and free, responsible, rationally credible mind on the other. I again clip as an in a nutshell:

    What we actually observe is:

    A: [material computational substrates] –X –> [rational inference]

    B: [material computational substrates] —-> [mechanically and/or stochastically governed computation]

    C: [intelligent agents] —-> [rational, freely chosen, morally governed inference]

    D: [embodied intelligent agents] —-> [rational, freely chosen, morally governed inference]

    The set of observations A through D imply that intelligent agency transcends computation, as their characteristics and capabilities are not reducible to:

    – components and their device physics,
    – organisation as circuits and networks [e.g. gates, flip-flops, registers, operational amplifiers (especially integrators), ball-disk integrators, neuron-gates and networks, etc],
    – organisation/ architecture forming computational circuits, systems and cybernetic entities,
    – input signals,
    – stored information,
    – processing/algorithm execution,
    – outputs

    >> and on the other hand you are claiming that the paper describing the synthesis of a genome>>

    g: Intelligently designed, recoding based synthesis of a complete genome, published in Nature.

    >> by an embodied being>>

    h: As opposed to an inferred, wholly materialistic computational entity based on a computational substrate.

    >> is a breakthrough for ID.>>

    i: Yes, a concrete, published demonstration of the intelligent design of a whole genome. Duly published in Nature.

    j: Thus, demonstration that intelligent design of major components of cell based life is possible, without thereby committing myself to any specific ontology or identity of candidate designers.

    k: One establishes arson as responsible process before embarking on identifying suspects and building a case. (Something that now seems to be a big problem, there is far too much of tainting projection by ill founded accusation followed by scapegoating.)

    KF

  280. 280
    Brother Brian says:

    279 comments on an OP about an ID breakthrough that a couple people disagree with. I don’t have the time just now but I would like to compare a word count of those who disagree with KF against a KF word count.

    In the immortal words of someone… “ Me thinks thou dost protest too much”. Far, far, far, far, far, far, far, far, far, far, far, far, far, far, far, far, far, far, far, far, far, far too much.

  281. 281
    hazel says:

    kf writes, “a: See the ideologically loaded, question-begging inference that human beings are material as opposed to embodied entities?”

    kf, Dave pointed out a long time ago that human beings are definitely material beings, but saying that does not mean they are exclusively materials beings: I for one believe that our minds, which are part of our being, are immaterial. Human beings are embodied beings. The main point being argued is that the OP doesn’t add any evidence that someplace along the way some purely immaterial, non-embodied being, designed life.

  282. 282
    Brother Brian says:

    Hazel, and please note that my inference is limited to embodied beings (not material beings). That is why I am mystified by KF’s emotional reaction to my proposed inference. OK, to be honest, I’m not mystified. I completely expected it. But I expected it because I know that KF’s ID inference has never acknowledged the possibility that the designer isn’t his God.

  283. 283
    Brother Brian says:

    Hazel, please note that my inference is limited to embodied beings (not material beings). That is why I am mystified by KF’s emotional reaction to my proposed inference. OK, to be honest, I’m not mystified. I completely expected it. But I expected it because I know that KF’s ID inference has never acknowledged the possibility that the designer isn’t his God.

  284. 284
    Ed George says:

    KF, it certainly looks like people are siding with BB over you on this pointless debate. Sometimes, when everyone disagrees with you, even your supporters (where are they, by the way?), a wise man would admit defeat. Or, at least, admit that they were wrong.

  285. 285
    kairosfocus says:

    BB:

    No substantial response, as predicted.

    EG:

    The issues stand on the merits.

    H:

    The context is clear, it is notorious that evolutionary materialistic scientism is a dominant though ill-founded ideology. When one wishes to bind intelligence to embodiment, that context is patently in the subtext. Therefore it is relevant to address this issue.

    Secondly, by showing that rationally inferring intelligence is categorically distinct from computation on a substrate, it is warranted to reject the attempt to bind intelligence like that.

    In that context, we may return focus to where it began; design being demonstrated, it is possible and should not be ideologically locked out.

    KF

  286. 286
    daveS says:

    KF,

    Do you have any hopes of design by a non-embodied designer being demonstrated in real time, in a laboratory setting?

  287. 287
    kairosfocus says:

    DS, my hopes or not-hopes are irrelevant. KF

  288. 288
    hazel says:

    Let’s rephrase the question: kf, do you think that it is possible that empirical evidence of current activity by a disembodied designer could be discovered? If so, what might that evidence look like?

  289. 289
    kairosfocus says:

    H, the fine tuned cosmos, set to a deeply isolated operating point enabling C-Chem, aqueous medium, cell-based life. In addition, there are any number of miracles including of healing that have been observed. Many of these have medical evidence. Just, the dominant evolutionary materialism and linked radical secularism tend to suppress widespread awareness in certain circles. A classic paper is here.Of course, the world of life is full of functionally specific, complex organisation and/or information, but such is not decisive as to ontological nature of designers. The examination of the ontology and identity of designers is a wider question than the focal one of reliable identification of design as causal process on signs. Surrounding circumstances such as design being antecedent to the observed cosmos may be relevant. KF

  290. 290
    hazel says:

    The “finely-tuned cosmos” is not current, I’ll note. And what kind of “medical evidence” shows that a miracle was done by an immaterial designer?

    And this quote at the end of the paper you linked to is pertinent:

    No attempt has been made to prove that miracles have occurred, such proof being probably impossible. The adjective “miraculous” is, however, permissible as a convenient shorthand for an otherwise almost inexplicable healing which occurs after prayer to God and brings honour to the Lord Jesus Christ.”

    I don’t think this counts as “empirical evidence”, and certanly not “in the laboratory”

    Conclusion: kf’s reply to the statement that all instances of design that we have experienced have come from embodied designers is to offer religiously-based counter examples of the supposed actions of God. That’s not very convincing.

    I really am not too interested in all this, as it has gone a long way from the OP (remember the OP?), but has been revealing to me.
    These cases have bee

  291. 291
    hazel says:

    Ooops. Bad formatting on that last post.

    The “finely-tuned cosmos” is not current, I’ll note. And what kind of “medical evidence” shows that a miracle was done by an immaterial designer?

    And this quote at the end of the paper you linked to is pertinent:

    No attempt has been made to prove that miracles have occurred, such proof being probably impossible. The adjective “miraculous” is, however, permissible as a convenient shorthand for an otherwise almost inexplicable healing which occurs after prayer to God and brings honour to the Lord Jesus Christ.”

    I don’t think this counts as “empirical evidence”, and certanly not “in the laboratory”

    Conclusion: kf’s reply to the statement that all instances of design that we have experienced have come from embodied designers is to offer religiously-based counter examples of the supposed actions of God. That’s not very convincing.

    I really am not too interested in all this, as it has gone a long way from the OP (remember the OP?), but has been revealing to me.

  292. 292
    Brother Brian says:

    KF

    No substantial response, as predicted.

    When you have something of substance to respond to, I will do so. Until then we have the fact that my inference is as strong (if not stronger) than the ID inference. Every bit of design, CSI, irreducible complexity that has a confirmed source, an embodied being. As such the best explanation for life, if it was designed, is an embodied being. That is how inferences work.

    Even if I were to concede that fine tuning proves the existance of an extra cosmic intelligence, which I don’t (see Adam’s sentient puddle analogy to see the absurdity of the claim), that has no affect on the strength of my inference until you can find some evidence for this extra cosmic intelligence interacting with the material world.

  293. 293
    kairosfocus says:

    H, fine tuning evidence is both current and emergent, never mind that origins of the observed cosmos may be 13.8 BYA, or whatever the latest suggested date is. Also, insofar as such speaks to world root necessary being, that carries with it the implications of necessary being. Next, there is a difference between proof of factual and witnessed events beyond all doubt and adequate warrant for moral certainty — which has long since been passed. Miracles involve intentional, intelligent and often information rich events so are relevant; miracles in answer to prayer, e.g. as Gardner documents, show cases of evidently intelligent action beyond the normal course of nature not involving any embodied candidate agent, e.g. consider the woman who should have bled out her blood volume. The relevant timeline on origins of the world of life are such that you have the logic back-ways: it is reliable signs of intelligent action here and now (embodiment being irrelevant as repeatedly shown) that allow us to confidently infer such on traces from OoL and Oo body plans, many of which are manifest in genomes. More could be said, but it’s budget season, pardon. KF

  294. 294
    Brother Brian says:

    KF

    miracles in answer to prayer, e.g. as Gardner documents, show cases of evidently intelligent action beyond the normal course of nature not involving any embodied candidate agent,

    There was a randomized double blind study done on the effectiveness of prayer in recovery from heart surgery. One group was prayed for. One was not prayed for, and the third was not prayed for but they were told that they were. There was no significant differences in recovery for the first two groups. However, the third group had a marginally better recover outcome. Placebo is a wonderful thing. If there is a benefit to prayer it has the same cause as the placebo effect, not an intervening God.

  295. 295
    kairosfocus says:

    BB, the usual skeptical dismissals fail on these and many other cases. One factor you overlook is that you are exchanging messages with someone who, absent miraculous guidance in answer to my mom’s prayer of surrender, would be dead 50 years since. Many, many others have similar life transforming encounters with God that hyperskeptical dismissiveness would dismiss. But when the scale of what is being dismissed runs to many millions and to millennia, that begins to imply that the ideology entails grand delusion, thus is self-refuting by leading to general discredit of rationality. Another factor you overlook in your “study” is that prayer is a moral imperative (not the saying of magic words) as well as it is inherently request of one whose wisdom exceeds ours, so a design that selects those to pray for and those NOT to pray for is morally indefensible and undermines any claimed prayers. Such a study fails from the outset. This reflects a wider pattern where ever so many fail to think through implications of our inescapably known duties to truth, right reason, prudence, fairness and justice etc. KF

    PS: This is responding to your incidental concerns, it is not embarking on a theological debate.

  296. 296
    daveS says:

    It is remarkable how this being whose presence is obvious to many is able to completely avoid detection in the laboratory.

  297. 297
    Brother Brian says:

    KF

    BB, the usual skeptical dismissals fail on these and many other cases.

    Only in KF world could citing a research paper from Harvard be classified as “skeptical dismissal”?

    One factor you overlook is that you are exchanging messages with someone who, absent miraculous guidance in answer to my mom’s prayer of surrender, would be dead 50 years since.

    I must have missed that research paper in the journals. Do you have a citation?

  298. 298
    ET says:

    Brother Brian:

    Every bit of design, CSI, irreducible complexity that has a confirmed source, an embodied being. As such the best explanation for life, if it was designed, is an embodied being. That is how inferences work.

    You don’t have any idea how inferences work. If you did then you would have realized that if it could not have been an embodied being then clearly that being was something else.

    (see Adam’s sentient puddle analogy to see the absurdity of the claim)

    LoL! That analogy is pure absurdity. Your desperation is showing, again.

  299. 299
    ET says:

    Brother Brian:

    1) All confirmed examples of design are the result of an intelligent being (humans).

    That is false. Termite mounds are the result of an intelligent being that is not a human. Bee hives; ant colonies; beaver dams- there are many, many example of non-human intelligence designing things.

    But again, that misses the point. If it could not have been an animal from earth then we infer it was some other form of intelligence.

    THAT is how inferences work.

  300. 300
    ET says:

    daves:

    It is remarkable how this being whose presence is obvious to many is able to completely avoid detection in the laboratory.

    That’s the blind watchmaker for you. Its presence is obvious to the willfully ignorant and yet it fails in the lab.

  301. 301
    ET says:

    daves:

    Do you have any hopes of design by a non-embodied designer being demonstrated in real time, in a laboratory setting?

    So you need absolute proof? Strange that you don’t demand that from your side. Also science isn’t about absolute proof, so you lose, again.

    What is missing from science is any evidence of design by blind and mindless processes, in real time, in a lab setting.

  302. 302
    daveS says:

    ET,

    So you need absolute proof?

    I don’t know how you arrived at that conclusion, but no.

  303. 303
    hnorman42 says:

    BB @ 292 –
    I am familiar with Douglas Adams’ analogy of the sentient puddle. But that is a tautology. A puddle fits its hole by definition. Its probability of doing so is 1. So it doesn’t address the problem of specified complexity at all.

  304. 304
    ET says:

    Earth to daves- this is how I arrived at that conclusion:

    Do you have any hopes of design by a non-embodied designer being demonstrated in real time, in a laboratory setting?

    Duh

  305. 305
    daveS says:

    ET,

    My post didn’t say anything about “absolute proof”. Just evidence analogous to that presented in the Nature article, except involving a designer without a physical body.

  306. 306
    ET says:

    daves:

    My post didn’t say anything about “absolute proof”

    Yes, it did.

    Just evidence analogous to that presented in the Nature article, except involving a designer without a physical body.

    Absolute proof.

  307. 307
    daveS says:

    ET,

    So the Nature article comprises absolute proof? That’s interesting, in view of your statement:

    Also science isn’t about absolute proof, so you lose, again.

  308. 308
    ET says:

    daves:

    So the Nature article comprises absolute proof?

    It absolutely proves that humans can synthesize a genome.

    That’s interesting, in view of your statement:

    Except it isn’t mine. Try learning the history of science.

  309. 309
    daveS says:

    It absolutely proves that humans can synthesize a genome.

    I guess it’s not science, then. Who knew?

  310. 310
    ET says:

    daves:

    I guess it’s not science, then.

    It was more akin to engineering.

  311. 311
    daveS says:

    ET,

    Well, whatever it was, I asked about a similar demonstration involving a non-embodied designer. That sort of “live” example would be persuasive.

  312. 312
    ET says:

    Yes, daves, you aren’t interested in science. There are plenty of haunted places in this world. Go visit them for your non-embodied designer.

  313. 313
    daveS says:

    Haunted places? Have you witnessed any? While this is a bit tangential to the OP, any appearance of a non-embodied being in our world would be of interest to many of us.

  314. 314
    ET says:

    The evidence is there. And there is more evidence, by far, for non-embodied intelligence then there is for the blind watchmaker.

  315. 315
    kairosfocus says:

    DS,

    the publication in Nature is a record of testimony, through a reputable agency. For the fact that the synthesis was done and much as described it can be taken as providing moral certainty. On this, there are no good grounds to lock out consideration of design as a serious, credibly feasible causal factor on origin of cell based life. Which immediately discredits a long term campaign that has notoriously sought to do just that. The absence of facing painful facts on yet another shameful recent chapter in science, education, media and courts etc is itself telling.

    Next, I find the rhetorical attempt to re-set the issue at stake, credibly understanding and assessing alternative views on origins (here, mainly OoL) to debating non-embodied intelligences in the here-now an interesting case of side-tracking. There is good reason why a great many people consider evolutionary materialistic scientism to be wrong-headed, self-refuting and domineering all rolled in one. There is also good reason why many people consider the current reality and observed action of non-embodied intelligences to be empirical reality. But given the dominance and domineering nature of secularist thought, we can expect dismissiveness.

    But that is immaterial to something I am exploring in a second thread: https://uncommondescent.com/animal-minds/logic-first-principles-21-insightful-intelligence-vs-computationalism/

    Namely, while computationalism and linked binding of intelligent action to computational substrates is a dominant view, it is in fact seriously, fundamentally flawed. My core, summary reasons lie in:

    What we actually observe is:

    A: [material computational substrates] –X –> [rational inference]
    B: [material computational substrates] —-> [mechanically and/or stochastically governed computation]
    C: [intelligent agents] —-> [rational, freely chosen, morally governed inference]
    D: [embodied intelligent agents] —-> [rational, freely chosen, morally governed inference]

    The set of observations A through D imply that intelligent agency transcends computation, as their characteristics and capabilities are not reducible to:

    – components and their device physics,
    – organisation as circuits and networks [e.g. gates, flip-flops, registers, operational amplifiers (especially integrators), ball-disk integrators, neuron-gates and networks, etc],
    – organisation/ architecture forming computational circuits, systems and cybernetic entities,
    – input signals,
    – stored information,
    – processing/algorithm execution,
    – outputs

    This was brought up above but was not cogently addressed by objectors. And yet it is central: When A is itself on certain characteristics and B is diverse on its own characteristics, we have reason to distinguish A and B. In this case, ontologically. Hence, the force of Reppert on the failure of computation to account for rational contemplation:

    . . . let us suppose that brain state A [–> notice, state of a wetware, electrochemically operated computational substrate], which is token identical to the thought that all men are mortal, and brain state B, which is token identical to the thought that Socrates is a man, together cause the belief [–> concious, perceptual state or disposition] that Socrates is mortal. It isn’t enough for rational inference that these events be those beliefs, it is also necessary that the causal transaction be in virtue of the content of those thoughts . . . [But] if naturalism is true, then the propositional content is irrelevant to the causal transaction that produces the conclusion, and [so] we do not have a case of rational inference. In rational inference, as Lewis puts it, one thought causes another thought not by being, but by being seen to be, the ground for it. But causal transactions in the brain occur in virtue of the brain’s being in a particular type of state that is relevant to physical causal transactions.

    That is, we have no good reason to bind freely rational, morally governed contemplation to mechanically and stochastically driven, controlled and bound computation. So, even with an embodied intelligence, embodiment and associated computational substrates do not properly account for intelligence.

    In this context, inference to design for OoL etc is not bound to embodiment, even in the hypothetical case where 4 BYA the equivalent to Venter working in an orbital molecular nanotech lab synthesised cell based life on earth. Why? Because the embodiment is not causally adequate and does not allow us to bind intelligence to embodiment.

    That’s been pointed out above many times, just not substantially addressed.

    Then, is the design inference just a way to put a divine foot in the door?

    No, we are just respecting logic of being issues and noting that intelligence is not ontollogically, causally bound to embodiment.

    KF

  316. 316
    daveS says:

    KF,

    the publication in Nature is a record of testimony, through a reputable agency. For the fact that the synthesis was done and much as described it can be taken as providing moral certainty. On this, there are no good grounds to lock out consideration of design as a serious, credibly feasible causal factor on origin of cell based life.

    Agreed. I certainly am not attempting to lock out anything.

    Next, I find the rhetorical attempt to re-set the issue at stake, credibly understanding and assessing alternative views on origins (here, mainly OoL) to debating non-embodied intelligences in the here-now an interesting case of side-tracking. There is good reason why a great many people consider evolutionary materialistic scientism to be wrong-headed, self-refuting and domineering all rolled in one. There is also good reason why many people consider the current reality and observed action of non-embodied intelligences to be empirical reality. But given the dominance and domineering nature of secularist thought, we can expect dismissiveness.

    I am not dismissing the notion that non-embodied intelligences actually exist and are active in our world. I find the idea fascinating. But I have never seen a hint of such a thing, while several of my friends have, which adds to the mystery.

    That is, we have no good reason to bind freely rational, morally governed contemplation to mechanically and stochastically driven, controlled and bound computation. So, even with an embodied intelligence, embodiment and associated computational substrates do not properly account for intelligence.

    Agreed. I don’t think anyone here is making such a claim.

  317. 317
    kairosfocus says:

    F/N: I clip from the parallel thread, for those inclined to take the rhetorical attempts above to distance embodiment and trying to bind intelligent rational thought to computational substrates at anything near to face value:

    Computationalism,
    Connectionism, and the
    Philosophy of Mind
    Brian P. McLaughlin

    The central questions of the philosophy of mind
    are the nature of mental phenomena, and how
    mental phenomena ?t into the causal structure
    of reality. The computational theory of mind
    aims to answer these questions. The central tenet
    of the theory is that a mind is a computer. Ac-
    cording to the theory, mental states and events
    enter into causal relations via operations of the
    computer. The main aim of the theory is to say
    what kind of computer – what kind of computa-
    tional mechanism – a mind is. The answer is still
    unknown. Pursuing it is the main research pro-
    gram of the theory.
    In the most general sense, a computer is,
    roughly, a system of structures functionally
    organized in such a way as to be able to com-
    pute. The structures, their functional organiza-
    tion, and the basic modes of operation of the
    system when it computes comprise the functional
    architecture of the computer. The two tasks of
    the computational theory of mind are: (1) to
    identify the functional architecture of the com-
    puting system that grounds our mental abilities
    and (2) to explain how those abilities are exer-
    cised via operations of the system.

    That’s why Reppert’s A is A i/l/o its characteristics, not B given its sharply diverse characteristics is so relevant and powerful.

    KF

  318. 318
    kairosfocus says:

    DS, you are not the locus of the problem, a dominant school of thought and its wide shadow of influence is. As I just pointed out. KF

    PS: Read and ponder Plato’s parable of the cave.

  319. 319
    daveS says:

    KF,

    DS, you are not the locus of the problem

    Complete and total exoneration. 🙂

  320. 320
    Brother Brian says:

    H

    I am familiar with Douglas Adams’ analogy of the sentient puddle. But that is a tautology. A puddle fits its hole by definition. Its probability of doing so is 1. So it doesn’t address the problem of specified complexity at all.

    It wasn’t used to address specified complexity. It is just an analogy of the argument of “fine tuning” of the universe being proof of God.

  321. 321
    Brother Brian says:

    DaveS

    I am not dismissing the notion that non-embodied intelligences actually exist and are active in our world. I find the idea fascinating. But I have never seen a hint of such a thing, while several of my friends have, which adds to the mystery.

    Try prayer. If it kept KF alive 50 years ago, surely it will facilitate your seeing of evidence for a non-embodied intelligence. 🙂

  322. 322
    OLV says:

    Transcription factor–DNA binding: beyond binding site motifs

    recent studies have elucidated additional layers of complexity that modulate TF–DNA binding.

    additional layers of complexity?

    🙂

  323. 323
    ET says:

    Brother Brian:

    It is just an analogy of the argument of “fine tuning” of the universe being proof of God.

    It failed as an analogy of “fine tuning”. It exposes the desperation of those who cannot explain the fine tuning.

  324. 324
    ET says:

    daves:

    But I have never seen a hint of such a thing, …

    Do the research then. It has to be easy enough to find allegedly haunted places and visit them.

  325. 325
  326. 326
    daveS says:

    The follow-on thread just blew wide open:

    Wha’ happen?

  327. 327
    Brother Brian says:

    DaveS

    Wha’ happen?

    KF has invoked dimension-f to explain why it is impossible for humans to synthesize a living, thinking human being from scratch. If you don’t know what dimension-f is, just picture an old guy in the sky who looks just like God.

  328. 328
    daveS says:

    Brother Brian,

    It looks like something blew wide open over there.

  329. 329
    Axel says:

    Dave S, your post #9:
    ‘I would call this intelligent modification, not intelligent design.’
    ——————–
    Indeed. It is ‘intelligent modification of design’ ; and is it not singularly propitious that the original design is intelligible enough to be seamlessly modified by the input of a human mind ? It is altering the ‘plan’, also known by its synonym, ‘design’.

  330. 330
    Axel says:

    Your #65, ET :
    ‘And guess what? No one has ever observed nature producing a genome.’ – ET

    Are you not forgetting the demi-urges of animisim that animate everything, ET ? They have been notoriously difficult to track down. Even the photographs of the alleged fairies at the bottom of a garden have been revealed as a hoax by one of its perpetrators, but so what, eh ? We know they are canny creatures – just as suely as we know evamolution is established science.

  331. 331
    kairosfocus says:

    BB, it is almost amusing to see the gap between your summary and what I actually discussed. I have pointed out, on cause, why true rationality requires a supervisory oracle that is non algorithmic, non computational; on pain of Reppert’s reductio applying. I take it you and others accept that we are genuinely rational, which requires transcending computationalism, where also emergentism is unstable, sliding into computationalism or else being synonymous to a non computational supervisory oracle. You and others latched on to the zygote, and particularly a proposed synthetic one and pressed on the matter as I pointed out that this is now speculative territory. In that context, I spoke to how we could conceive of a non-computational entity through the window of a fifth dimension, [x,y,z,t,f] so could see how something like that could interface with loci in 4-d common space in context of a two-tier controller cybernetic loop. In addition, I spoke to quantum influence and raised the point that the zygote to begin with and onward the human body across its lifespan could be viewed as having a portal, an interface through which such could engage the biological entity; remember, it was you who went speculative, I am responding with a conceptual model that may open up room for thought — and I took time to compare how moving from a 3-d view of the earth to a 3-d one brings to bear the astonishing properties of the N-pole as a way to see how dimensionality changes things . . . I assume you have read Flatland. Further, I pointed to the Casimir effect as an example of quantum influence effects. In that context, I invited participation in a potential consilience. So, your distorted out of context sketch tells me a few things. KF

  332. 332
    hazel says:

    kf is offering a different way, admittedly speculative, of understanding how the biological, material zygote obtains the immaterial qualities of rationality, free will, etc.

    But the questions still remains: if we built a genome from scratch that copied in it essentials the human genome, but perhaps with some intelligently designed changes, would a person with that genome automatically have access to this other dimension, and thus obtain rationality, et al? That is, does the existence of a material being open the door, so to speak, to these qualities even if that being was not produced by procreation?

  333. 333
    kairosfocus says:

    H, The possibility of a quantum portal raises issues of one had better understand what he is doing. That’s part of what a model like that helps us look for. It is likely there are aspects to the zygote we do not know, basically don’t have a clue about. Synthesis of a genome using synonyms may be problematic [the slowdown with E coli is a warning sign], synthesis of a whole cell, we already know is way beyond. It seems a lot of knowledge base would have to be built up and there are truly serious ethical issues with attempted synthesis of a human zygote. I suspect the wise thing is to outright ban that. If it were tried under likely circumstances, outcomes will be a lottery; get it right enough and the portal might work, if it is there. And I note, something is there as we are rational and this is beyond computational substrates.The question is, what is there, and animal analogues may be of limited utility. That, again, is part of what a model like this may throw up. KF

  334. 334
    Brother Brian says:

    KF

    Synthesis of a genome using synonyms may be problematic…

    Nobody was talking about synonyms. The scenario was to synthesize a human genome and grow it to an adult. The genome can be s complete duplicate of an existing human.

    synthesis of a whole cell, we already know is way beyond.

    Yet you have already said that you believe this will be done in the near future.

    Everything you have presented so far is pure speculation and, possibly, wishful thinking. All of the evidence suggests that if we can ever synthesize a complete human genome and somehow have it develop into a living, breathing human, it will be every bit as human as you and I.

    And with regard to imposing some undefined extra dimension (God) to produce reasoning and free will, why are humans the only animals (supposedly) to have it?

  335. 335
    kairosfocus says:

    BB,

    by skipping threads the actual record keeps getting distorted.

    I responded to what I saw and understood in the other thread, which means this follow on session here lacks context.

    In any case, my point stands, that we are dealing with the problem of rationality, where neither straight materialist accounts, nor weak emergentism (mind comes along for the ride) can answer to the issue of needing to transcend limitations of computational substrates as Reppert highlights. Strong emergentism lacks the mechanism it needs, and is effectively a concession of a supervisory oracle of essentially different character than a computational substrate.

    Next, while I believe that we may advance to synthesis of a cell — and I had in mind primarily unicellular organisms — within 100 years (as can be seen above) I do not underestimate the magnitude of the task, and on the human case, the issue of transcendence implied in our rationality and moral government. There is something much more to this case, hence the points raised in response to your pressing in the succeeding thread.

    Third, of course there is a speculative element, you and others insisted on going into matters where we do not have empirical evidence, putting up a scenario of synthesis and demanding what-ifs. I repeatedly pointed that out and you all kept pressing, as you obviously thought it advantageous. So, I responded by putting up a possibility and model then inviting us to consider a possible consilience, on which, thread hopping. Fair comment, you have here played, you hit back first. Sorry, on that record, you don’t get to now play the catch-22 game gotcha if you don’t, gotcha if you do.

    The fundamental issue of the credible mind is on the table, tied to origin of a human, embodied being from the zygote on.

    Tell me why I should reject the concept that the form of the rational minded being and the bodily substance should not be present together from conception on: ______ and tell me why I should not follow researchers who point to quantum influences as a likely candidate to be the basis for mind-body interaction? (Which you experience by reading and typing out responses.) ___________

    And, I note, you have used that isolation of my response on your insistence and that of others, to spread an aura of wishful thinking which implicitly extends to what is backed by something that is based on the experience of the human race. Namely, that we are genuinely rational; which per physics of computational substrates, cannot be accounted for on computationalism. This is the context where I used the Smith model to draw out how a supervisory oracle (suggested as interfacing through quantum influences — and note the Casimir effect on how such phenomena are real in surprising ways) that is not algorithmic or a composite carrying out a computational process is needed to break the undermining of rational freedom that follows from dynamics of mechanical and/or stochastic interactions of components.

    I need to ask you directly: are we genuinely, freely rational and responsible? ________ If so, given your acknowledged evolutionary materialism, how is this accounted for i/l/o issues Reppert and others have raised? _______ If not, then does not that imply that a reasonable, responsible discussion is impossible, reducing a community of discussion to grand delusion as say Crick and Rosenberg as cases in point imply? ___________ Why/why not? _________

    Indeed, this goes further: to be deluded, one must form a world-picture and accept it as materially true when it is false. This implies a lot of capabilities to be self-aware and to form beliefs etc, i.e. a deluded mind is till a mind. So, if our mindedness reduces to the action of a wetware computational substrate (refined, organised rock processing signals etc) then, how do we get to minded self-aware contemplation enough to form beliefs, even delusional ones: ___________

    In this context, I find it reasonable to take rationality seriously. Then, to reckon with its credibly non-computational nature, based on rational understanding, inferences, intentions, etc, all under moral government. This, through undeniably known duties to truth, right reason, prudence (so, warrant), fairness and justice etc. So, our minds operate under moral government, as an aspect of their essential freedom. That is, on both sides of the IS-OUGHT gap. That points to the need to bridge that gap, which is only feasible in the roots of reality. This sets out a bill of requisites: independent existence (so, necessary being), adequacy to found a world such as we inhabit, adequacy to found oughtness as inherent to that being. Thus, inherently good.

    In that light, everything changes.

    KF

    PS: Provide cases in point, kindly, of other creatures in our observation that exhibit full rationality including use of symbolic language that deals with abstracta: ________ Then, kindly show where anyone has argued above that we are the only possible such creatures: _________ I think we are a clear example of rational animality [that’s our hylemorphic description, noting what anima actually means at root] but as contingent creatures we cannot exhaust the set of possible cases. Indeed, on the evidence that mindedness is not accounted for on computational substrates, we do not have a good reason to hold that rationality requires embodiment.

  336. 336
    hazel says:

    kf writes, ” nor weak emergentism (mind comes along for the ride) ”

    FTR, that description of what I have suggested minimizes, distorts, and inaccurately portrays what I have suggested. Just sayin’.

  337. 337
    kairosfocus says:

    H, I was not describing you in particular, I spoke to forms of emergentism where mind is an epiphenomenon that shadows the underlying physical, causally connected states. This is Reppert’s direct target. Strong form emergentism does have in it top down cause, i.e. mind over matter, but has no account of origins of mind that allow the emergence in any credible fashion. Thus, it becomes a form of mind over matter dualism. This is why I stated that emergentism is inherently unstable, falling back into physicalist reductionism (which is self-referentially absurd) or else becoming — often unrecognised or sometimes unacknowledged — a form of dualism. Compatibilist accounts of volitional freedom tend to be emergentist, often weak form. This of course is a vest pocket, in a nutshell, boiled down summary of reams of technical discussions out there. KF

  338. 338
    hazel says:

    OK, I stand corrected. I don’t think mind is an epiphenomena.

  339. 339

    Dualism only became a standard philosophical position because at one time it was entirely rational and justifiable to believe that matter existed and was largely irreconcilable with mind without some kind of proposed interface. We know now that matter does not exist; that the perception of “matter” is entirely an experience within mind because it entirely breaks down, when examined closely enough via quantum physics research, into nonphysical potentials governed by the nature of the consciousness involved. IOW, there is no “there” there. Dualism is dead, and so is all of the problematic baggage and issues associated with it. Pity we’re still employ that term and inserting it into arguments.

  340. 340
    kairosfocus says:

    WJM, You raise concerns that tie to the enduring question of THE ONE AND THE MANY, how do we resolve unity and diversity in a world with room for human significance. Materialist monism fails, and the instability of emergentism shows part of why, direct Crick or Rosenberg [etc] style reductionism of mind to matter or viewing the mind as not having top-down causal capability undermine both rationality and responsibility, ending in grand delusion. This leads to how strong emergentism [whether software or hardware driven] becomes a poof-magic version of dualism, lacking a cogent account of the emergence and credibility of mind. On the other hand, mental monism is also problematic, leading to the implication that the world we experience is a Matrix-like dream. I suggest instead that seeing our minds and bodies as integrated from outset and with interface that permits influences, is a more fruitful way. One that can reckon with the evidence of a designed cosmos rooted in a necessary and intelligent, powerful designer, where being the root of oughtness points to being also essentially good. Where, necessity of being implies not composite based on organisation of distinct proper parts, so immaterial. Also, ability to reason and design implies mind as ultimate supervisory oracle, a free agent, a mind.Matter being a product of mind, is then credibly accessible to the influence of mind, where the concept of quantum influence discussed briefly in the other thread opens up a possible way for such. In that context, we would be embodied, minded creatures, where the concept of a wholeness involving intimate union as rational beings with integral supervisory oracles [= minds, with consciences etc] opens up possibilities. KF

  341. 341
    kairosfocus says:

    H, responsible rationality of an embodied bio-cybernetic significantly free, top-down acting self-moved agent [i.e. we see a supervisory oracle of non-computational character] points to amphibian, mind over matter being. Where, as morally governed beings we operate on both sides of the IS-OUGHT gap. In turn, that points to the root of reality as the only place such can be bridged. We need as root, a necessary [causally independent, non composite] being capable of causing a cosmos and being of inherently good character. KF

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