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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.

Comments
PaoloV @342, Still waiting for an answer to your question? Don't hold your breath. :)jawa
June 23, 2019
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Biological robustness? Another strong argument supporting ID: Emerging Perspectives from within the Life Sciences Introduction: Issues About Robustness in the Practice of Biological Sciences
Robustness has lately become a bridging notion, in particular across the sciences of the natural and the artificial, crucial for prediction and control of natural and artificial systems in recent scientific practice, in biomedicine, neurobiology and engineering, as well as for risk management, planning and policy in ecology, healthcare, markets and economy. From biological, neurological and societal systems, arising by the interplay of self-organizing dynamics and environmental pressures, to the current sophisticated engineering that aims at artificially reproducing the adaptability and resilience of living systems in front of perturbations in man-made devices, robustness seems to hold the key for orchestrating stability and change. This introduction offers a general survey of the contribution that the notion of robustness is providing to reframing major concepts within the life sciences, such as development, evolution, time and environment, and to reframing the relationship between biology and engineering, as well as between biology and physics.
Prolegomena to a History of Robustness
The paper outlines a historical reconstruction of the spread of the concept of robustness across different disciplinary fields, and of the major significant shifts, which comprise the stratigraphy of the semantic expansion of this notion. Starting from the emergence of the modern notion in statistics, which inspired also its actual epistemic instantiations, the paper examines the historical relationship between dynamical systems theory and the notion of robustness, and analyzes the developments that prompted the shift from “modern” to “robust” control theory in engineering. It further deals with the first instantiations of the concept in biology in the 1990s, in order to highlight the turn impressed on the concept by Systems Biology, focusing particularly on its implications as to the relationship between robustness and complexity.
Robustness, Mechanism, and the Counterfactual Attribution of Goals in Biology
The first part of this paper discusses two important meanings of robustness (robustness as stability as against variations in parameter values and robustness as consilience of results from different sources of evidence) and shows their essential connection with the notion of intersubjective reproducibility. As I shall maintain, robustness in both senses of the term is intimately connected with the notion of scientific experiment. This is the important element of truth of the mechanistic systems approach, which explains events as products of robust and regular systems and processes. In the second part of this paper I shall show that the concept of robustness of a mechanism, if applied to biological systems, is one-sided and incomplete without a heuristic?methodical reference to final causes, even though the assumption of the teleological point of view is justified in biology only to the extent that we use it as a counterfactual artifice, capable of bringing to light causal relations which have a robustly reproducible content. In this way, the reflexive, typically human concept of purposefulness may be employed to investigate living beings scientifically, that is, in an intersubjectively testable and reproducible way, to discover mechanisms in living systems which are robust in both senses of the word.
Multiple Realization and Robustness
Multiple realization has traditionally been characterized as a thesis about the relation between kinds posited by the taxonomic systems of different sciences. In this paper, I argue that there are good reasons to move beyond this framing. I begin by showing how the traditional framing is tied to positivist models of explanation and reduction and proceed to develop an alternate framing that operates instead within causal explanatory frameworks. I draw connections between this account and the notion of functional robustness in biology and neuroscience. I then examine two cases from systems neuroscience that substantiate my account and show how traditional debates fail to track important features of these cases.
Robustness: The Explanatory Picture
Robustness is a pervasive property of living systems, instantiated at all levels of the biological hierarchies (including ecology). As several other usual concepts in evolutionary biology, such as plasticity or dominance, it has been questioned from the viewpoint of its consequences upon evolution as well as from the side of its causes, on an ultimate or proximate viewpoint. It is therefore equally the explanandum for some enquiries in evolution in ecology, and the explanans for some interesting evolutionary phenomena such as evolvability. This epistemological fact instantiates general property of biological evolution that I call “explanatory reversibility”. In this chapter, I attempt to systematize the explanatory projects regarding robustness by distinguishing a set of epistemological questions. Are they the various expressions of one general project with specific key concepts and methods, or very disparate epistemic projects, unified by the mere homonymy of the term “robustness”? More precisely, are there specific kinds of explanations suited to explain robustness? Finally, how does robustness as an explanandum connect with other explananda in which evolutionists have been massively interested recently such as complexity, modularity or evolvability? After having initially explored various meanings of the concept of robustness and surveyed its instances in biology, I will propose a distinction between mechanical and structural explanations of robustness in evolutionary and functional biology. Then, among the latter, I will highlight the class of “topological explanations,” and the subclass of explanations based on networks, as a major explanatory tool to address robustness. Focusing on evolutionary issues, I will eventually address the “explanatory reversibility” of robustness and consider its relation to key evolutionary concepts that are also explanatorily revertible such as modularity, evolvability and complexity.
Robustness and Autonomy in Biological Systems: How Regulatory Mechanisms Enable Functional Integration, Complexity and Minimal Cognition Through the Action of Second-Order Control Constraints
Living systems employ several mechanisms and behaviors to achieve robustness and maintain themselves under changing internal and external conditions. Regulation stands out from them as a specific form of higher-order control, exerted over the basic regime responsible for the production and maintenance of the organism, and provides the system with the capacity to act on its own constitutive dynamics. It consists in the capability to selectively shift between different available regimes of self-production and self-maintenance in response to specific signals and perturbations, due to the action of a dedicated subsystem which is operationally distinct from the regulated ones. The role of regulation, however, is not exhausted by its contribution to maintain a living system’s viability. While enhancing robustness, regulatory mechanisms play a fundamental role in the realization of an autonomous biological organization. Specifically, they are at the basis of the remarkable integration of biological systems, insofar as they coordinate and modulate the activity of distinct functional subsystems. Moreover, by implementing complex and hierarchically organized control architectures, they allow for an increase in structural and organizational complexity while minimizing fragility. Finally, they endow living systems, from their most basic unicellular instances, with the capability to control their own internal dynamics to adaptively respond to specific features of their interaction with the environment, thus providing the basis for the emergence of minimal forms of cognition.
Robustness and Emergent Dynamics in Noisy Biological Systems
The concepts of robustness and stability play a central role in many natural phenomena ranging from Astrophysics up to Life. In this contribution we discuss these concepts by specifically focusing on a biological paradigmatic mathematical model for the nonlinear electrophysiology of clusters of animal beta-cells.
The Robustness/Sensitivity Paradox: An Essay on the Importance of Phase Separation
Considering biological systems at different levels of organization as complex networks in which nodes (genes, proteins, metabolites…) are each other connected by (co-expression, physical interactions) is a very natural way of reasoning. Network approach allows scientist to make sense of the intricacies of biological regulation and, for the same mathematical nature of graphs, to obtain a multilevel description linking single node and whole network topological features. This paradigm allows for the detection of a clear signature of robustness: the ability of a system to keep separate different scales of response to environmental stimuli. A case study on the immune system allows for an immediate appreciation of this point.
Can Engineering Principles Help Us Understand Nervous System Robustness?
Nervous systems are formidably complex networks of nonlinear interacting components that self organise and continually adapt to enable flexible behaviour. Robust and reliable function is therefore non-trivial to achieve and requires a number of dynamic mechanisms and design principles that are the subject of current research in neuroscience. A striking feature of these principles is that they resemble engineering solutions, albeit at a greater level of complexity and layered organisation than any artificial system. I will draw on these observations to argue that biological robustness in the nervous system remains a deep scientific puzzle, but not one that demands radically new concepts.
Robustness vs. Control in Distributed Systems
Understanding and controlling the behavior of dynamical distributed systems, especially biological ones, represents a challenging task. Such systems, in fact, are characterized by a complex web of interactions among their composing elements or subsystems. A typical pattern observed in these systems is the emergence of complex behaviors, in spite of the local nature of the interaction among elements in close spatial proximity. Yet, we point out that each element is a proper system, with its inputs, its outputs and its internal behavior. Moreover, such elements tend to implement feedback control or regulation strategies, where the outputs of a subsystem A are fed as inputs to another subsystem B and so on until, eventually, A itself is influenced. Such complex feedback loops are understood only by considering, at the same time, low- and high-level perspectives, i.e., by regarding such systems as a collection of systems and as a whole, emerging entity. In particular, dynamical distributed systems show nontrivial robustness properties, which are, from one side, inherent to the each subsystem and, from another, depend on the complex web of interactions. In this chapter, therefore, we aim at characterizing the robustness of dynamical distributed systems by using two coexisting levels of abstraction: first, we discuss and review the main concepts related to the robustness of systems, and the relation between robustness, model and control; then, we decline these concepts in the case of dynamical distributed systems as a whole, highlighting similarities and differences with standard systems. We conclude the chapter with a case study related to the chemotaxis of a colony of E. Coli bacteria. We point out that the very reason of existence of this chapter is to make accessible to a vast and not necessarily technical audience the main concepts related to control and robustness of dynamical systems, both traditional and distributed ones.
The Robustness of Musical Language: A Perspective from Complex Systems Theory
Within the field of systems theory, the term robustness has typically been applied to different contexts such as automatic control, genetic networks, metabolic pathways, morphogenesis, and ecosystems. All these systems involve either man-made machines, or living organisms. In this chapter, we will consider music as a peculiar complex system, involving both the realm of machines (the musical instrument) and the realm of biology (the player and the listeners). We will discuss some of the properties of music experience in terms of different attributes of robustness, focusing in particular on stability, the property enabling a complex system to maintain its function against a wide range of external and internal changes. We will provide examples of the human ability of isolating and maintaining stable information within the perceptual flow and despite changes in the external world that reach our perceptions, leading towards a characterization of robustness in music perception as referred both to the search for regularities and to the range of tolerance that perception admits to regularities. Finally, we will list four multiple interaction cycles that typically characterize music experience and that involve both internal properties of the organism and the environment.
Dynamical Rearrangement of Symmetry and Robustness in Physics and Biology
The mechanism of the dynamical rearrangement of symmetry in quantum field theory underlies the phenomenon of coherent boson condensation in the vacuum state. Coherent states appear to be related to fractal self-similarity. The dynamical paradigm of coherence opens the way to an integrated vision of natural phenomena and it may possibly rule morphogenetic processes. Robustness properties of physical systems, such as dynamical and functional robustness, topological robustness, multilevel and semantic robustness may find their root in coherence. Possible extension to biology and neuroscience is discussed.
Difference and Robustness: An Aristotelian Approach
The paper starts by recalling the ordinary and etymological sense of the word “robustness”, for placing it then in the context of the current systemic view. Then I focus discussion on systems robustness in the paradigmatic case of living organisms. We discover that the notion of robustness is closely linked, in the case of organism, with the notion of difference, given that organisms arise precisely by a differentiation process (Sect. 13.1). So, in order to understand the ontology of robustness, we need to explore the ontology of difference; and in order to do so, we must distinguish between constitutive and comparative difference (Sect. 13.2.1). Then I deal with the problem of unity of the constitutive differences: I wonder if it is possible to unify the many differences that an organism exhibits in a single difference. It is an important question, given that unity is one of most essential characteristics of the organism (Sect. 13.2.2). And the answer to this question raises immediately a query for the intelligibility of this final and unique constitutive difference (Sect. 13.2.3). Such intellibility is possible thanks to the formal nature of the final difference, but it requires also a pluralistic approach. Besides that, we have to sketch the ontological and epistemological relationships between difference, identity and similarity (Sect. 13.3), which will be crucial for intelligibility of the difference, since according to a certain tradition, intelligibility depends on identity.
OLV
June 17, 2019
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339 WJM @339:
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.
Still haven't heard the answer to this simple hypothetical question: Would WJM (a) look both ways before crossing a bi-directional road or (b) ignore any fast approaching truck as just an immaterial experience within mind?PaoloV
June 17, 2019
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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. KFkairosfocus
June 4, 2019
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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. KFkairosfocus
June 4, 2019
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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.William J Murray
June 3, 2019
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OK, I stand corrected. I don't think mind is an epiphenomena.hazel
June 3, 2019
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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. KFkairosfocus
June 3, 2019
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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'.hazel
June 3, 2019
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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.kairosfocus
June 3, 2019
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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?Brother Brian
June 2, 2019
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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. KFkairosfocus
June 2, 2019
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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?hazel
June 2, 2019
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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. KFkairosfocus
June 2, 2019
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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.Axel
June 2, 2019
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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'.Axel
June 2, 2019
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Brother Brian, It looks like something blew wide open over there.daveS
June 2, 2019
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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.Brother Brian
June 2, 2019
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The follow-on thread just blew wide open:
Wha' happen?daveS
June 2, 2019
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F/N: The follow-on thread just blew wide open: https://uncommondescent.com/animal-minds/logic-first-principles-21-insightful-intelligence-vs-computationalism/#comment-678042 KFkairosfocus
June 2, 2019
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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.ET
May 29, 2019
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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.ET
May 29, 2019
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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? :)OLV
May 29, 2019
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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. :)Brother Brian
May 29, 2019
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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.Brother Brian
May 29, 2019
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KF,
DS, you are not the locus of the problem
Complete and total exoneration. :)daveS
May 29, 2019
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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.kairosfocus
May 29, 2019
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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. KFkairosfocus
May 29, 2019
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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.daveS
May 29, 2019
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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. KFkairosfocus
May 29, 2019
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