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L&FP, 62: The Systems (and Systems Engineering) Perspective — a first step to understanding design in/of our world

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Our frame going forward, is knowledge reformation driven by application of the adapted JoHari Window, given obvious, fallacy-riddled ideological captivity of the intellectual high ground of our civilisation:

Ideological captivity of the high ground also calls forth the perspective that we need to map the high ground:

If you want some context on validity:

So, we are now looking at ideologically driven captivity of the intellectual high ground and related institutions of our civilisation, leading to compromising the integrity of the knowledge commons through fallacy riddled evolutionary materialistic scientism and related ideologies. Not a happy thought but that is what we have to deal with and find a better way forward.

We already know, knowledge (weak, everyday sense) is warranted, credibly true (so, reliable) belief, and that it is defeasible on finding gaps or errors that force reworking. Classically, that happened twice with Physics, the shattering of the Scholastic view through the Scientific revolution, and the modern physics revolution that showed limitations of newtonian dynamics and classical electromagnetism. Physics, like Humpty Dumpty [and the underlying fallen Roman Empire], has never been put back together again.

But, how do we proceed?

Through systems thinking and systems engineering, on several levels.

First, NASA defines:

“systems engineering” is defined as a methodical, multi-disciplinary approach for the design, realization, technical management, operations, and retirement of a system. A “system” is the combination of elements that function together to produce the capability required to meet a need. The elements include all hardware, software, equipment, facilities, personnel [–> thus, these are sociotechnical systems and bridge engineering and management], processes, and procedures needed for this purpose; that is, all things required to produce system-level results. The results include system-level qualities, properties, characteristics, functions, behavior, and performance. The value added by the system as a whole, beyond that contributed independently by the parts, is primarily created by the relationship among the parts; that is, how they are interconnected. [–> functional, information rich organisation adds value] It is a way of looking at the “big picture” when making technical decisions. It is a way of achieving stakeholder functional, physical, and operational performance requirements in the intended use environment over the planned life of the system within cost, schedule, and other constraints. It is a methodology that supports the containment of the life cycle cost of a system. In other words, systems engineering is a logical way of thinking.

Systems engineering is the art and science of developing an operable system capable of meeting requirements within often opposed constraints. Systems engineering is a holistic, integrative discipline

NASA has a big scoping chart for Systems Engineering in a project/programme management context:

We can look at the Systems Engineering Vee Model (HT: ResearchGate):

Another view, notice, the implied, layer cake modularity of systems, from physical materials to base devices and components [consider a transistor or a bolt], to function units, to system modules and organisation to overall functionality based on information rich organisation:

U/D, Oct 13: We may add a chart on a key subset of SE, reverse engineering, RE:

A summary of RE, HT: Global Spec (We may often start with step 2, and obviously Step 1 has a typo for purpose, a little RE exercise in itself.)

One of the most significant RE-FE exercises was the clean room duplication of the IBM PC’s operating framework that allowed lawsuit-proof clones to be built that then led to the explosion of PC-compatible machines. By the time this was over, IBM sold out to Lenovo and went back to its core competency, Mainframes. Where, now, a mainframe today is in effect a high end packaged server farm; the microprocessor now rules the world, including the supercomputer space.

Here, let us add, a Wikipedia confession as yet another admission against interest:

Reverse engineering (also known as backwards engineering or back engineering) is a process or method through which one attempts to understand through deductive reasoning [–> actually, a poor phrase for inference to best explanation, i.e. abductive reasoning] how a previously made device, process, system, or piece of software accomplishes a task with very little (if any) [–> initial] insight into exactly how it does so. It is essentially the process of opening up or dissecting [–> telling metaphor] a system [–> so, SE applies] to see how it works, in order to duplicate or enhance it. Depending on the system under consideration and the technologies employed, the knowledge gained during reverse engineering can help with repurposing obsolete objects, doing security analysis, or learning how something works.[1][2]

Although the process is specific to the object on which it is being performed, all reverse engineering processes consist of three basic steps: Information extraction, Modeling, and Review. Information extraction refers to the practice of gathering all relevant information [–> telling word, identify the FSCO/I present in the entity, and of course TRIZ is highly relevant esp its library of key design strategies] for performing the operation. Modeling refers to the practice of combining the gathered information into an abstract model [–> that is, the inferred best explanation], which can be used as a guide for designing the new object or system. [–> guess why I think within this century we should be able to build a cell de novo?] Review refers to the testing of the model to ensure the validity of the chosen abstract.[1] Reverse engineering is applicable in the fields of computer engineering, mechanical engineering, design, electronic engineering, software engineering, chemical engineering,[3] and systems biology.[4] [More serious discussion, here.]

We can see that

one paradigm for science is, reverse engineering nature.

This directly connects to, technology as using insights from RE of nature to forward engineer [FE] our own useful systems. And of course that takes us to a theme of founders of modern science, that they were “thinking God’s thoughts after him.”

In that SE-RE-FE context, we can bring on board issues of systems architecture and related matters, as I commented earlier today:

An Analogue Computer network with two chained integrators

Computer architecture at first level, is the study of the assembly/machine language view, i.e. information, its processing [including coding, algorithmic processes etc], associated function units, their organisation. Underlying physical science and technique to effect these units carries us to the layer cake, modular network, systems view. With analogue computers, the focus is on continuous state function units and how they represent key mathematical operations [famously, integration] that then integrate in a process flow network to handle continuous state information bearing signals and materials or states and phases of dynamic stochastic entities etc. This extends the context to instrumentation, control and systems engineering as well as telecommunications, bringing in frequency domain transforms and approaches as well as state/phase space approaches. These give us fresh eyes to see and more objectively understand the molecular nanotech marvels in the cell.

Obviously, this immediately allows us to reconsider the cell as a marvel of nanotechnology, e.g. here is its metabolic framework, part of how it is a metabolising, molecular nanotech self replicating automaton:

Just the top left corner, already involves a complex algorithmic process using coded information:

Protein Synthesis (HT: Wiki Media)

Then, there is the communication network this expresses, as Yockey pointed out:

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

All of this, we have known for decades, but now it is time to independently ponder it as a system and understand how this exemplifies and instantiates such system elements. We can immediately set aside crude fallacies of appeals to dismissible analogies, once we ponder, say, the genetic code as just that, a 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

Just for reference, by fair use doctrine, here is Lehninger’s comparison:

By starting from a systems perspective, we can then rebuild knowledge on a sounder footing than the present ideologically driven institutional capture. END

110 Replies to “L&FP, 62: The Systems (and Systems Engineering) Perspective — a first step to understanding design in/of our world

  1. 1
    kairosfocus says:

    L&FP, 62: The Systems (and Systems Engineering) Perspective — a first step to understanding design in/of our world

  2. 2
    kairosfocus says:

    F/N: I added the Lehninger comparison of a Cuneiform Stele with DNA bursting out of a bacterium.

  3. 3
    kairosfocus says:

    F/N3: From Acknowledgements, to help us understand the significance and weight of Lehninger:

    Fifty years ago, Al Lehninger published the ?rst edition of Biochemistry, de?ning the basic shape of biochemistry courses worldwide for generations. We are honored to have been able to carry on the Lehninger tradition since his passing in 1986, now introducing the eighth (our seventh) edition of Lehninger Principles of Biochemistry.

    FYI

    KF

  4. 4
    Seversky says:

    We acknowledge the existence of design in the Universe. We do it.

    We acknowledge the possibility of extraterrestrial design but we have no evidence for it at this time.

    We acknowledge the appearance of design in nature but only the appearance based on analogies with human artefacts.

    We acknowledge that the great complexity observed in the natural world still lacks a compelling explanation of origins.

    We acknowledge that the naturalistic approach to science has proven more fruitful than any alternatives.

    We acknowledge that the Intelligent Design/Creationist rejection of methodological naturalism in favor of creationist explanations is a form of selective hyper-skepticism similar to that of which science is accused.

  5. 5
    jerry says:

    We acknowledge etc.

    Actually, a mantra that ID pretty much agrees with but the distortion creeps in at the end

    It should be

    We acknowledge that the Intelligent Design rejection of methodological naturalism in favor of intelligence explanations for a small number of phenomena is a form of skepticism similar to that of which science is based.

  6. 6
    relatd says:

    Seversky at 4,

    Nonsense. At the Mayo Clinic and elsewhere, guess what? The ASSUMPTION made by brainwashed Biologists had to be discarded to make actual progress in identifying the sources of human disease. How are they doing that? By looking at Junk DNA. By studying it. Not throwing it out as ‘leftovers from our long [alleged] period of Evolution.’ By studying it as opposed to ‘it doesn’t code for proteins so it’s useless.’ Those so-called non-coding regions are yielding vital information about human disease, The “natural” approach discarded them – without looking.

  7. 7
    kairosfocus says:

    Sev, if we needed confirmation on the point, you just gave it . . . DV, overnight. KF

  8. 8
    kairosfocus says:

    Sev, do you realise how much you gave away, by how unresponsive you have been to not only the substance in the OP or discussion over the years or even the weak argument correctives? Message: you felt a need to lay out the standard, strawman and ad hom laced talking points to trigger the standard evolutionary materialistic scientism and fellow traveller narrative, to dismiss what you object to. That game is now over.

    On your talking points, in — “deconstructive” — steps of thought:

    >>We acknowledge the existence of design in the Universe. We do it.>>

    1- Why, yes, just by composing a complex text you exhibited a central sign of design, functionally specific, complex organisation and/or associated information [FSCO/I], y’know, the same that objectors every now and then pretend is not real or observable, cannot be defined to their satisfaction, can be dismissed on the usual “no evidence” claim.

    2- But in fact you know just as well as we do that such FSCO/I exists and we have a trillion member base of observations of its only actually observed source, intelligently directed configuration, let’s abbreviate IDC, aka “design.” Also, requiring “intelligence”:

    Merriam Webster:
    Definition of intelligence

    1a(1) : the ability to learn or understand or to deal with new or trying situations : reason also : the skilled use of reason
    (2) : the ability to apply knowledge to manipulate one’s environment or to think abstractly as measured by objective criteria (such as tests) . . .

    3 : the act of understanding : comprehension [–> notably, creative use of language expresses intelligence]

    3- Where, too, we all know that simple analysis of blind search challenge in large config spaces beyond the inference threshold, 500 – 1,000 bits [3.27^10^150 to 1.07*10^301 possible configurational states] shows that the only plausible source is such IDC.

    4- That is, we have a well tested highly reliable sign of design and are epistemically entitled to infer that the best explanation — absent clear actually observed counter-example of blind dynamic stochastic process [aka blind chance and/or mechanical necessity] producing FSCO/I — on observing FSCO/I is IDC.

    5- Of course, neither you nor many other longstanding critics have ever provided an actual counter example that meets the actual observed cause Newton’s rules that work to prune speculation pretending to be observationally anchored science.

    6- In short, you and ever so many other objectors know you have no answer to this central observationally anchored inference on good, reliable sign. So, you rhetorically dodge, set up and knock over a strawman caricature instead. (Notably, in the OP, Lehninger and/or heirs give a direct comparison between an Assyrian Stele and DNA in a cell.)

    7- Further, that design exists and designers exist implies that responsible, rational significant freedom exists, which carries even more with it as this points to the logic of being of a contingent world with such creatures and its causal roots. Especially, with a world full of signs of fine tuning.

    8- Of course, the Lehninger example is telling: beyond reasonable, responsible dispute, applying reverse engineering principles [REP] of systems engineering [SE], we see complex, alphanumeric, algorithmic code in the heart of the cell, implying language, text — they explicitly discuss text — stepwise goal directed process, numerically controlled molecular nanotech machinery in sophisticated organisation and fulfilling a metabolising, von Neumann kinematic self replicator automaton. On RE, Wikipedia confesses:

    Reverse engineering (also known as backwards engineering or back engineering) is a process or method through which one attempts to understand through deductive reasoning [–> actually, a poor phrase for inference to best explanation, i.e. abductive reasoning] how a previously made device, process, system, or piece of software accomplishes a task with very little (if any) [–> initial] insight into exactly how it does so. It is essentially the process of opening up or dissecting [–> telling metaphor] a system [–> so, SE applies] to see how it works, in order to duplicate or enhance it. Depending on the system under consideration and the technologies employed, the knowledge gained during reverse engineering can help with repurposing obsolete objects, doing security analysis, or learning how something works.[1][2]

    Although the process is specific to the object on which it is being performed, all reverse engineering processes consist of three basic steps: Information extraction, Modeling, and Review. Information extraction refers to the practice of gathering all relevant information [–> telling word, identify the FSCO/I present in the entity, and of course TRIZ is highly relevant esp its library of key design strategies] for performing the operation. Modeling refers to the practice of combining the gathered information into an abstract model [–> that is, the inferred best explanation], which can be used as a guide for designing the new object or system. [–> guess why I think within this century we should be able to build a cell de novo?] Review refers to the testing of the model to ensure the validity of the chosen abstract.[1] Reverse engineering is applicable in the fields of computer engineering, mechanical engineering, design, electronic engineering, software engineering, chemical engineering,[3] and systems biology.[4] [More serious discussion, here.]

    9- Thus, replete with FSCO/I including the additionality of the vNSR facility. See, REP and so SE at work? Language and goal directed process are particularly strong signs of design. Designers, for example have goals.

    >>We acknowledge the possibility of extraterrestrial design but we have no evidence for it at this time.>>

    10- In the face of a real SETI wow signal, right in the cells of our bodies, with multiple Nobel Prize winners on public record, the no evidence stunt is pulled out.

    >>We acknowledge the appearance of design in nature>>

    11- Oh yes, the invitation to use REP of SE is that blatant.

    >> but only the appearance based on analogies with human artefacts.>>

    12- A twisted caricature of the design inference on observed, tested, reliable signs and refusal to recognise REP of SE.

    13- We instantiate design, but manifestly, we are contingent creatures with signs of design in our bodies, pointing to onward designers. And, for millennia there has been an ongoing literature on the blatantly manifest possibility of other designers so the penumbra of objectors cannot be ignorant of this.

    14- So, to the signs we should go.

    15- Where of course the analogies stunt is a way to wave away what for example Lehninger and heirs highlight as a case of parallel instantiation. As in, right there in the OP.

    >>We acknowledge that the great complexity observed in the natural world still lacks a compelling explanation of origins.>>

    16- Translated, refusing to attend to REP of SE and to telling signs of design, we must concede that we have no empirically well founded blind chance and/or mechanical necessity driven explanation of causal origin of:

    * a fine tuned cosmos fitted for C-Chem, aqueous medium, cell based life
    * the sophisticated polymer chem in said cells
    * the complex integrated system constituting a molecular nanotech metabolising automaton with vNSR
    * the coded alphanumeric information and text in D/RNA, expressing inter alia algorithms with nanotech execution machines such as the ribosome
    * thus, OoL, after a century of active research
    * thence, too, Oo body plans, OoBP
    * also, origin of our own body plan and mindedness enabling rational responsible freedom and ability to create knowledge
    * and more

    >>We acknowledge that the naturalistic approach to science has proven more fruitful than any alternatives.>>

    17- The usual, we succeeded in reverse engineering nature claim, but much of this is stolen valour and stolen achievement, pretending that Science is applied atheism. In fact a simple survey of the origin and outworking of modern science will show this to be a fundamentally dishonest caricature.

    18- Philip Johnson’s reply to Lewontin’s cat out of the bag moment is telling:

    For scientific materialists the materialism comes first; the science comes thereafter. [Emphasis original — the context is Lewontin in NYRB] We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence.

    [–> notice, the power of an undisclosed, question-begging, controlling assumption . . . often put up as if it were a mere reasonable methodological constraint; emphasis added. Let us note how Rational Wiki, so-called, presents it:

    “Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific “dead ends” and God of the gaps-type hypotheses.” [NB: I am aware that Rational Wiki has backed away, un-announced, from the cat-out-of-the-bag direct phrasing that was in place a few years ago. That historic phrasing is still valid as a summary of what is going on.]

    Of course, this ideological imposition on science that subverts it from freely seeking the empirically, observationally anchored truth about our world pivots on the deception of side-stepping the obvious fact since Plato in The Laws Bk X, that there is a second, readily empirically testable and observable alternative to “natural vs [the suspect] supernatural.” Namely, blind chance and/or mechanical necessity [= the natural] vs the ART-ificial, the latter acting by evident intelligently directed configuration. [Cf Plantinga’s reply here and here.]

    And as for the god of the gaps canard, the issue is, inference to best explanation across competing live option candidates. If chance and necessity is a candidate, so is intelligence acting by art through design. And it is not an appeal to ever- diminishing- ignorance to point out that design, rooted in intelligent action, routinely configures systems exhibiting functionally specific, often fine tuned complex organisation and associated information. Nor, that it is the only observed cause of such, nor that the search challenge of our observed cosmos makes it maximally implausible that blind chance and/or mechanical necessity can account for such.]

    That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.”

    . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [Emphasis added.] [The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

    19- Of course, dodged, side stepped and evaded for twenty-five years.

    20- Instead, we apply a more realistic paradigm: Science is in many regards, reverse engineering of our world.

    >>We acknowledge that the Intelligent Design/Creationist>>

    21- Here comes ad hominem by slanderous conflation of two fundamentally distinct movements.

    22- Creationists generally refers to people who start with the Bible as a text viewed as report of the Creator and seek to explain phenomena on that thesis. The design inference is a REP of SE exercise, on grounds that we can see on the face, well known signs of design. So, let us do RE of nature, asking if it makes sense and is effective,

    23- ans, yes especially if science seeks to learn truth about our world on open ended empirical investigation — rather than imposing an a priori ideological frame such as Lewontin-Crick-Monod-Mahner-NSTA-NAS evolutionary materialistic scientism. Methodologically. completely different.

    24- Once the general public understands that science has been ideologically, politically captured to advance radical secularist agendas, there will be hell to pay, for good reason. Especially given that it is the taxes of the despised, ruthlessly manipulated hoi polloi that have been funding this mutiny on the ship of state.

    25- Let me venture a suggestion, the jumping the shark moment is going to be the mismanaged pandemic with its ideological capture of the lab and medical coat.

    >>rejection of methodological naturalism in favor of creationist explanations>>

    26- Ad hom laced strawman caricature and slander sustained in the teeth of longstanding, repeated correction.

    27- Narrative like this will always eventually fall in the face of truth.

    >> is a form of selective hyper-skepticism>>

    28- A silly attempt at turnspeech, turnabout projection.

    29- Pointing out that abduction controlled by requiring that suggested causes be actually seen to work, is prudence requiring adequate warrant per observation, not hyperskepticism.

    30- But, thanks for the confession by projection to the other.

    >>similar to that of which science is accused.>>

    31- Evolutionary Materialistic scientism and its implicit theme that science is applied atheism, is not equal to science.

    32- The pretence that observed hyperskepticism, such as “EXTRAORDINARY claims require extraordinary [–> adequate] evidence,” is “science” has long since passed its sell-by date.

    KF

  9. 9
    Alan Fox says:

    Jerry suggests an amended version of Seversky’s declaration;

    We acknowledge that the Intelligent Design rejection of methodological naturalism in favor of intelligence explanations for a small number of phenomena is a form of skepticism [my emphasis] similar to that of which science is based.

    A small number of phenomena? I’m curious, Jerry. Which phenomena are you suggesting that methodological naturalism is the wrong approach to investigate?

  10. 10
    kairosfocus says:

    F/N: On the stolen valour, stolen achjevement point, to forestall a cheap turnabout, I put on the table an excerpt from Dan Peterson:

    Sometimes the most obvious facts are the easiest to overlook. Here is one that ought to be stunningly obvious: science as an organized, sustained enterprise arose only once in the history of Earth. Where was that? Although other civilizations have contributed technical achievements or isolated innovations, the invention of science as a cumulative, rigorous, systematic, and ongoing investigation into the laws of nature occurred only in Europe; that is, in the civilization then known as Christendom. Science arose and flourished in a civilization that, at the time, was profoundly and nearly exclusively Christian in its mental outlook.

    There are deep reasons for that, and they are inherent in the Judeo-Christian view of the world which, principally in its Christian manifestation, formed the European mind. As Stark observes, the Christian view depicted God as “a rational, responsive, dependable, and omnipotent being and the universe as his personal creation, thus having a rational, lawful, stable structure, awaiting human comprehension.” That was not true of belief systems elsewhere. A view that the universe is uncreated, has been around forever, and is just “what happens to be” does not suggest that it has fundamental principles that are rational and discoverable. Other belief systems have considered the natural world to be an insoluble mystery, conceived of it as a realm in which multiple, arbitrary gods are at work, or thought of it in animistic terms. None of these views will, or did, give rise to a deep faith that there is a lawful order imparted by a divine creator that can and should be discovered.

    [–> Clue: why do we still talk about “Laws” of nature? Doesn’t such historically rooted language not suggest: a law-giver? (And indeed, that is precisely what Newton discussed at length in his General Scholium to his Mathematical Principles of Natural Philosophy.) Of course, that will not move the deeply indoctrinated and polarised, but it is a clear marker to those who are willing to think more open-mindedly.]

    Recent scholarship in the history of science reveals that this commitment to rational, empirical investigation of God’s creation is not simply a product of the “scientific revolution” of the 16th and 17th centuries, but has profound roots going back at least to the High Middle Ages . . . .

    Albertus Magnus — prodigious scholar, naturalist, teacher of Thomas Aquinas, and member of the Dominican order — affirmed in his De Mineralibus that the purpose of science is “not simply to accept the statements of others, that is, what is narrated by people, but to investigate the causes that are at work in nature for themselves.” Another 13th-century figure, Robert Grosseteste, who was chancellor of Oxford and Bishop of Lincoln, has been identified as “the first man ever to write down a complete set of steps for performing a scientific experiment,” according to Woods.

    WHEN THE DISCOVERIES of science exploded in number and importance in the 1500s and 1600s, the connection with Christian belief was again profound. Many of the trailblazing scientists of that period when science came into full bloom were devout Christian believers, and declared that their work was inspired by a desire to explore God’s creation and discover its glories. Perhaps the greatest scientist in history, Sir Isaac Newton, was a fervent Christian who wrote over a million words on theological subjects. Other giants of science and mathematics were similarly devout: Boyle, Descartes, Kepler, Leibniz, Pascal. To avoid relying on what might be isolated examples, Stark analyzed the religious views of the 52 leading scientists from the time of Copernicus until the end of the 17th century. Using a methodology that probably downplayed religious belief, he found that 32 were “devout”; 18 were at least “conventional” in their religious belief; and only two were “skeptics.” More than a quarter were themselves ecclesiastics: “priests, ministers, monks, canons, and the like.”

    Down through the 19th century, many of the leading figures in science were thoroughgoing Christians. A partial list includes Babbage, Dalton, Faraday, Herschel, Joule, Lyell, Maxwell, Mendel, and Thompson (Lord Kelvin). A survey of the most eminent British scientists near the end of the 19th century found that nearly all were members of the established church or affiliated with some other church.

    In short, scientists who were committed Christians include men often considered to be fathers of the fields of astronomy, atomic theory, calculus, chemistry, computers, electricity, genetics, geology, mathematics, and physics. In the late 1990s, a survey found that about 40 percent of American scientists believe in a personal God and an afterlife — a percentage that is basically unchanged since the early 20th century. A listing of eminent 20th-century scientists who were religious believers would be far too voluminous to include here — so let’s not bring coals to Newcastle, but simply note that the list would be large indeed, including Nobel Prize winners.

    Far from being inimical to science, then, the Judeo-Christian worldview is the only belief system that actually produced it. Scientists who (in Boyle’s words) viewed nature as “the immutable workmanship of the omniscient Architect” were the pathfinders who originated the scientific enterprise. The assertion that intelligent design is automatically “not science” because it may support the concept of a creator is a statement of materialist philosophy, not of any intrinsic requirement of science itself.

    The redefinition of science in materialist terms — never wholly successful, but probably now the predominant view — required the confluence of several intellectual currents. The attack on religious belief in general, and Christianity in particular, has been underway for more than two centuries . . . . IT WAS THE AWE-INSPIRING SUCCESS of science itself, nurtured for centuries in a Christian belief system, that caused many to turn to it as the comprehensive source of explanation. With the mighty technology spawned by science in his hands, man could exalt himself, it seemed, and dispense with God. Although Darwin was by no means the sole cause of the apotheosis of materialist science, his theories gave it crucial support. It is perhaps not altogether a coincidence that the year 1882, in which Darwin died, found Nietzsche proclaiming that “God is dead…and we have killed him.”

    The capture of science (in considerable measure) by materialist philosophy was aided by the hasty retreat of many theists. There are those who duck any conflict by declaring that science and religion occupy non-overlapping domains or, to use a current catchphrase, separate “magisteria.” One hears this dichotomy expressed in apothegms such as, “Science asks how; religion asks why.” In this view, science is the domain of hard facts and objective truth. Religion is the realm of subjective belief and faith. Science is publicly verifiable, and is the only kind of truth that can be allowed in the public square. Religion is private, unverifiable, and cannot be permitted to intrude into public affairs, including education. The two magisteria do not conflict, because they never come into contact with each other. To achieve this peace, all the theists have to do is interpret away many of the central beliefs of the Judeo-Christian tradition.

    This retreat makes some theists happy, because they can avoid a fight that they feel ill-equipped to win, and can retire to a cozy warren of warm, fuzzy irrelevancy. It also makes materialists happy, because the field has been ceded to them. As ID advocate Phillip Johnson remarks acerbically:

    Politically astute scientific naturalists feel no hostility toward those religious leaders who implicitly accept the key naturalistic doctrine that supernatural powers do not actually affect the course of nature. In fact, many scientific leaders disapprove of aggressive atheists like Richard Dawkins, who seem to be asking for trouble by picking fights with religious people who only want to surrender with dignity.

    But the ID theorists do not go gentle into that good night. That’s what’s different about intelligent design. ID says that the best evidence we have shows that life is the product of a real intelligent agent, actually working in space and time, and that the designer’s hand can be detected, scientifically and mathematically, by what we know about the kinds of things that are produced only by intelligence. It is making scientific claims about the real world. Because it relies on objective fact and scientific reasoning, ID seeks admission to the public square. Rather than retreating to the gaseous realm of the subjective, it challenges the materialist conception of science on its own turf. It thus threatens materialism generally, with all that that entails for morality, law, culture — and even for what it means to be human.

    THOSE WHO NOW OCCUPY the public square will fight to keep possession of it. The advocates of Darwinian materialism believe that they are in possession of The Truth, and are perfectly willing to invoke the power of the state to suppress competing views [–> which should be a big warning-sign that something has gone very wrong] . . . [“What’s the Big Deal About Intelligent Design?” By Dan Peterson, American Spectator, Published 12/22/2005; also cf his earlier popular level summary on ID here. (HT: Wayback Machine.)]

    That can be backed up in detail, but let this stand up for now as a first summary.

    KF

  11. 11
    kairosfocus says:

    AF, actually, ANY phenomena as it is an expression of jumping the shark, ideological captivity. Mahner:

    http://www.springerlink.com/co......html#CR31

    . . . metaphysical naturalism is a constitutive ontological principle of science in that the general empirical methods of science, such as observation, measurement and experiment, and thus the very production of empirical evidence, presuppose a no-supernature principle [–> recall, we are dealing with what is institutionally dominant, it matters not that some would disagree, this is a statement of where the Overton Window lies and what the power brokers think they have power to lock out, regardless of actual merits] . . . .

    Metaphysical or ontological naturalism (henceforth: ON) [“roughly” and “simply”] is the view that all that exists is our lawful spatiotemporal world. Its negation is of course supernaturalism: the view that our lawful spatiotemporal world is not all that exists because there is another non-spatiotemporal world transcending the natural one, whose inhabitants—usually considered to be intentional beings—are not subject to natural laws . . . . Both scientists and science educators keep being challenged by creationists of all shades, who try hard to reintroduce supernaturalist explanations into biology and into all the areas of science that concern the origin of the world in general and of human beings in particular. [–> Confession by projection? No merely human power class has a permanent empire. This too will fall.]

    [–> of course he here glides by the point Plato highlighted in The Laws Bk X, natural vs supernatural, and the linked point that it is empirically well founded that there are signs of intelligently directed configuration as cause, where a major goal and condition of credibility of science is that it seeks empirically supported truth about our world. Ideological capture of science and science education potentially has a ruinous cost.]

    A major aspect of this debate is the role of ON in science . . . .

    ON is not part of a deductive argument in the sense that if we collected all the statements or theories of science and used them as premises, then ON would logically follow. After all, scientific theories do not explicitly talk about anything metaphysical such as the presence or absence of supernatural entities: they simply refer to natural entities and processes only. Therefore, ON rather is a tacit metaphysical supposition of science, an ontological postulate. It is part of a metascientific framework or, if preferred, of the metaparadigm of science that guides the construction and evaluation of theories, and that helps to explain why science works and succeeds in studying and explaining the world. [–> cat out of the bag.] [“The role of Metaphysical Naturalism in Science,” Science and Education, 2011]

    KF

  12. 12
    Alan Fox says:

    Oh the ignoance!

    The ASSUMPTION made by brainwashed Biologists had to be discarded to make actual progress in identifying the sources of human disease. How are they doing that? By looking at Junk DNA. By studying it. Not throwing it out as ‘leftovers from our long [alleged] period of Evolution.’ By studying it as opposed to ‘it doesn’t code for proteins so it’s useless.’ Those so-called non-coding regions are yielding vital information about human disease, The “natural” approach discarded them – without looking.

    Some people seem impervious to understanding. “Junk” DNA is not non-coding DNA. Non-coding DNA distinguishes DNA in genomes that do not get synthesized into proteins. About 1-2% of the human genome codes for proteins. Non-coding DNA, whilst not carrying sequences that become proteins, is nevertheless shown to be functional. Junk DNA is any DNA sequence that does not play a functional role in development, physiology, or some other organism-level capacity. [From here]

    I’d add more, but the Wikipedia article covers the basics.

  13. 13
    Alan Fox says:

    Your link is broken, KF.

  14. 14
    Alan Fox says:

    BTW, KF, your Johari window idea overlooks (insert pun here) one important and unbreachable fact. No sentient being (and I include you in that category) is capable of understanding any concept more complex than itself.

  15. 15
    kairosfocus says:

    AF,

    1- here is RG, now that they played the paywall game https://www.researchgate.net/publication/257662343_The_Role_of_Metaphysical_Naturalism_in_Science

    2- The assertion, cannot understand — at what level? — what is more complex than oneself fails the commonplace experience test: we have a useful measure of understanding of a world involving billions of creatures like ourselves, cumulatively far more complex than we are.

    3- Levels of understanding leads to recognising a difference between bounded error prone rationality and omniscience. Where the debates we have are mostly about the first three cells: the now needlessly broken knowledge commons, the imposition of error-warped agendas under colour of knowledge, the rise of a reformation movement.

    4- The unknown unknowns, known only to God take in what omniscience knows but also challenge us to open up frontiers through research. Not least as what we don’t know can hurt us badly.

    5- As a further challenge, we cannot exhaustively understand God, but we can understand him as an inherently good, utterly wise creator, a necessary and maximally great being worthy of respect, of loyalty and of the responsible, reasonable service of doing the good that accords with our evident nature.

    6- The adapted JoHari window does address unknown and known unknowns.

    7- Then there is what we refuse to acknowledge.

    KF

  16. 16
    kairosfocus says:

    F/N: I updated OP to add on reverse engineering. There is a diagram. KF

  17. 17
    kairosfocus says:

    AF, kindly note the Lehninger image on a stele vs DNA as text, in OP. KF

  18. 18
    jerry says:

    Which phenomena are you suggesting that methodological naturalism is the wrong approach to investigate?

    None.

    It just that the tools of science may not have an answer to the phenomena. So one has to look elsewhere for a possible answer. Every scientist admits there are phenomena that methodological naturalism cannot explain if it found they existed.

    ID does not suggest that typical scientific methods not be applied to every phenomenon. But there may be limits to what science can explain.

            That’s why ID is science+.

    It’s amazing I have to say this since it so obvious to either side from the beginning.

  19. 19
    relatd says:

    Jerry at 18,

    You still don’t see it? The COMMITMENT here is to repeat Evolution good, ID bad – forever. And to ignore any comments like yours as if they were never written.

  20. 20
    kairosfocus says:

    Relatd, meanwhile, we can forge ahead and address the emerging issues. First, the systems engineering perspective for example helps us to see scientific investigation as reverse engineering the world. From that we see how engineering is using the results and often imitates phenomena (sonar and radar vs bats and whales) or discovers that its principles and strategies are present in the world (finding algorithmic code and NC machines in the cell). This lends confidence in recognising design patterns and cases in the world. Thus, Lehninger and heirs have a point when they recognise that DNA is as much text as an Assyrian artifact. KF

  21. 21
    kairosfocus says:

    Calling Seversky . . .

  22. 22
    Alan Fox says:

    AF, kindly note the Lehninger image on a stele vs DNA as text, in OP. KF

    What do you want me to say? I can repeat the clear and indisputable fact that DNA encoding bears not even the most superficial comparison to human language. Does that help?

  23. 23
    Alan Fox says:

    Thus, Lehninger and heirs have a point when they recognise that DNA is as much text as an Assyrian artifact. KF

    If pressed, I doubt they could sustain that point (presuming it is the point, rather than your misinterpretation). I suspect it is an analogy that they introduce initially as window-dressing. As you demonstrate, the analogy is poor and adds nothing explanatory to how biology works.

  24. 24
    Alan Fox says:

    O/T

    Not that the appearance, evolution and nested relationships of human languages is not a fascinating subject in its own right. A closer look would perhaps persuade KF that the analogy between human languages and DNA coding falls apart on all levels

  25. 25
    kairosfocus says:

    AF, the point is clear and direct, tracing to Crick in 1953. It is not the lack of strength of the point — which they emphasised several times — that drives your objections but rejection of manifest fact because of import. The systems architecture is plain. The appeal to how “analogies” are fallacious, is what will fall apart on closer inspection. It is little more than the thin edge of a wedge to dismiss the inconvenience of observable patterns and inductive reasoning where it is not convenient. In short, your quarrel is with foundational principles of scientific reason, using logic with a swivel tactics of selective hyperskepticism. Here, you first posed on your claimed expertise in Biochem, then on being confronted with the views of senior experts, you are still trying to deflect the reasonable identification of digital, algorithmic information processing in protein synthesis. There is a reason why we recognise a genetic code and what a couple of dozen dialects. KF

  26. 26
    Alan Fox says:

    …rejection of manifest fact because of import.

    I’m saying the analogy between DNA coding is unhelpfully poor because it is. DNA sequences bear no similarity to human languages in any aspect of their function. You might claim that a written representation of human speech in a language known to the reader stores information and a DNA sequence may also store information but that’s it.

  27. 27
    kairosfocus says:

    AF, DNA code is an example of machine language, which is language used to effect algorithms. I have here no interest in Spanish, French, Latin, Esperanto or Volapuk (apart from their use of string data structure chains of glyphs ie alphanumeric code), but much interest in how machine code works. Your strawman distractor fails, you know a lot better than your rhetorical stunts. KF

  28. 28
    Alan Fox says:

    Tell me a word in DNA language. Put it in a sentence.

  29. 29
    Alan Fox says:

    Also , if I give you a DNA sequence, can you tell me what it says?

  30. 30
    kairosfocus says:

    AF, more on strawman tactics. You full well know what I just put up in a fresh OP: “we have AUG, START (and load Methionine), EXTEND (and load another specified AA), EXTEND . . . STOP.” Thus, we see algorithmic, machine code instructions in a recognisable case. That we may lack the depth of knowledge on polymer chemistry to readily predict function of a given AA string when folded, clumped together and suitably modified, does not detract from what we can and do know. Notice, my negative vs positive knowledge distinction here. Your refusal to acknowledge longstanding facts only serves to underscore their power in pointing to what you so obviously dread, design. KF

  31. 31
    Alan Fox says:

    Let me be more specific, then. Take Python. Tell me how python compares to DNA sequences. Give me an example of how DNA sequence is read as instruction. And let you be more specific too

  32. 32
    Alan Fox says:

    That we may lack the depth of knowledge on polymer chemistry to readily predict function of a given AA string when folded, clumped together and suitably modified, does not detract from what we can and do know.

    Well, that’s better. There’s no way to predict what DNA sequence “says” other than synthesizing the protein (futile for functional non-coding DNA) or comparing it to the growing database of known sequences. There’s no “language” there.

  33. 33
    Alan Fox says:

    we have AUG, START (and load Methionine), EXTEND (and load another specified AA), EXTEND . . . STOP

    *chuckles*

    Tell me, KF who is writing the code instructions, who or what is the instructor, and who or what is reading the code – who or what is being instructed? And try and stick to topics. I’ve been responding in the other thread.

  34. 34
    kairosfocus says:

    AF, you full well know Python is a high level, object oriented language. Such are compiled or interpreted into machine language specific to a particular CPU and its architecture. Similarly, you insist yet again on confounding observable machine code instructions — cf genetic code — and algorithms with onward issues. The obvious and due conclusion is that the observation is fatal to your preferred views. Duly, drawn. KF

  35. 35
    Alan Fox says:

    So now you claim is that DNA is written in machine code??? Goodness me!

  36. 36
    kairosfocus says:

    AF, your rhetorical stunts tell us the conclusion is well warranted. The Genetic Code gives us AA chain assembly instructions in an algorithmic context as well you know. That these AA chains are folded, clumped, modified etc to form proteins may be much less well understood, but that does not change what we do know and have known for decades. All your onward antics show is that these well established facts are fatal to your view. KF

  37. 37
    Alan Fox says:

    How is not why, KF.

    BTW, as you claim to know better than I do, what precisely is my view?

  38. 38
    kairosfocus says:

    AF, we both know that we are dealing with an algorithm. KF

  39. 39
    Alan Fox says:

    AF, we both know that we are dealing with an algorithm. KF

    No, KF, neither of us knowz that. An algorithm, briefly, might be defined as a precise set of instructions. So, tell me, KF, who or what is instructing and who or what is being instructed. I think I already asked you this.

  40. 40
    kairosfocus says:

    AF, you misdefined algorithm, which is a stepwise, finite goal directed procedure that halts. Which is what mRNA coming from DNA has. That is itself telling. KF

  41. 41
    Alan Fox says:

    AF, you misdefined algorithm…

    Did I? I plagiarized it from Wikipedia but there were many similar definitions. None mention the prerequisite to halt.

    …which is a stepwise, finite goal directed procedure that halts. Which is what mRNA coming from DNA has. That is itself telling. KF

    What are you saying about RNA (mRNA, I assume)? What does mRNA have, apart from a sequence of nucleotides? Which is it, instructor or instructed? I rather think mRNA is a molecule, myself.

  42. 42
    JVL says:

    Kairosfocus: we both know that we are dealing with an algorithm.

    What triggers the algorithm? Does it run all the time?

  43. 43
    kairosfocus says:

    AF,

    Wikipedia lead and onward excerpts, just now:

    In mathematics and computer science, an algorithm (/?æl??r?ð?m/ (listen)) is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation.[1] Algorithms are used as specifications for performing calculations and data processing. More advanced algorithms can perform automated deductions (referred to as automated reasoning) and use mathematical and logical tests to divert the code execution through various routes (referred to as automated decision-making) . . . . In general, a program is only an algorithm if it stops eventually[30] [–> finite, halting] —even though infinite loops may sometimes prove desirable. [ –> e.g. the main, polling loop in some computers, including the original Apple Mac that halts on an imposed interrupt such as power down.] . . . . Minsky: “But we will also maintain, with Turing … that any procedure which could “naturally” be called effective, can, in fact, be realized by a (simple) machine. Although this may seem extreme, the arguments … in its favor are hard to refute”.[37] Gurevich: “… Turing’s informal argument in favor of his thesis justifies a stronger thesis: every algorithm can be simulated by a Turing machine … according to Savage [1987], an algorithm is a computational process defined by a Turing machine”.[38] [–> of course, we would include supportive machines for the core processor etc]

    Finite of course implies halting. I explicitly included that as it is a significant issue. Goal-direction defines the intended target. A proper algorithm will include halt for abnormal states or the like.

    AmHD is especially good:

    A finite set of unambiguous instructions [= stepwise procedure, of course, coded] that, given some set of initial conditions [= start], can be performed in a prescribed sequence to achieve a certain goal [= goal-directed] and that has a recognizable set of end conditions [= halt].

    Of course mRNA is a string data structure that carries encoded AA chain algorithms, as well as other supportive structures. As noted, it uses molecular nanotech, based on polymer chemistry.

    KF

    PS, JVL, regulation of expression of the algorithm is onward from the fact of algorithm stored in mRNA and used in the ribosome to assemble AA chains as a stage of protein synthesis. That fact is pivotal. Since we are using Wiki’s confessions, on protein synthesis:

    Protein biosynthesis (or protein synthesis) is a core biological process, occurring inside cells, balancing the loss of cellular proteins (via degradation or export) through the production of new proteins. Proteins perform a number of critical functions as enzymes, structural proteins or hormones. Protein synthesis is a very similar process for both prokaryotes and eukaryotes but there are some distinct differences.[1]

    Protein synthesis can be divided broadly into two phases – transcription and translation. During transcription, a section of DNA encoding a protein, known as a gene, is converted into a template molecule called messenger RNA (mRNA). This conversion is carried out by enzymes, known as RNA polymerases, in the nucleus of the cell.[2] In eukaryotes, this mRNA is initially produced in a premature form (pre-mRNA) which undergoes post-transcriptional modifications to produce mature mRNA. The mature mRNA is exported from the cell nucleus via nuclear pores to the cytoplasm of the cell for translation to occur. During translation, the mRNA is read by ribosomes which use the nucleotide sequence of the mRNA to determine the sequence of amino acids [–> notice, algorithm]. The ribosomes catalyze the formation of covalent peptide bonds between the encoded amino acids to form a polypeptide chain.

    Following translation the polypeptide chain must fold to form a functional protein; for example, to function as an enzyme the polypeptide chain must fold correctly to produce a functional active site. In order to adopt a functional three-dimensional (3D) shape, the polypeptide chain must first form a series of smaller underlying structures called secondary structures. The polypeptide chain in these secondary structures then folds to produce the overall 3D tertiary structure. Once correctly folded, the protein can undergo further maturation through different post-translational modifications. Post-translational modifications can alter the protein’s ability to function, where it is located within the cell (e.g. cytoplasm or nucleus) and the protein’s ability to interact with other proteins.[3]

    Showing the thumb screws is very effective . . .

  44. 44
    Alan Fox says:

    And what has any of that to do with mRNA? Where’s the algorithm? What is instructing, what is being instructed, where are the instructions?

  45. 45
    kairosfocus says:

    AF, playing the you tell me card does not work, especially when there is already an excerpt on the table regarding protein synthesis, there are things in the OP on same and you full well know that AA chains to make proteins are assembled stepwise in the ribosome. All of this simply tells us that these readily found facts are fatal to your obvious evolutionary materialistic scientism and/or fellow traveller views. KF

  46. 46
    Alan Fox says:

    Ah, I’m a fellow traveller to Scientism, am I? KF, when you decide to start listening rather than pontificating, I may consider it worth interacting with you again.

  47. 47
    kairosfocus says:

    AF, so, oh, it’s pick up the ball and flounce out time. The excuse is, how dare you suggest I may be motivated by evolutionary materialistic scientism AND/OR ITS FELLOW TRAVELLERS. Which, is a fair comment, if it walks and quacks like a duck, reasonably accurate description of the dominant schools of thought of the day on origins. We can take it as confirmed that AF is uncomfortable with the facts on the table and with how things have turned out since he tried to play the it’s ignorance of biochem that makes you resort to saying the generic code is, err, ah, ahm, a code. Worse, one used to effect algorithms used for protein synthesis. Gambit failed. Sad, but sadly telling. KF

    PS, As a reminder, here is what Lehninger and heirs said a few pp on:

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

    See https://uncommondescent.com/darwinist-debaterhetorical-tactics/protein-synthesis-what-frequent-objector-af-cannot-acknowledge/

  48. 48
    Sir Giles says:

    AF: Ah, I’m a fellow traveller to Scientism, am I?

    You should be used to the rhetorical games by now. Label, assign motivation, polarize, dismiss, rinse, repeat.

  49. 49
    kairosfocus says:

    SG, predictable turnabout tactic to blame the target for daring to say unwelcome truth or fair comment; put up squid ink to escape behind. Implication, the real case has been lost on the merits, try to stain and irritate then escape; the just now talking points are a back handed concession, by way of confession by projection. The key clue being evasion and strawman tactics on substance. . Evolutionary materialistic [or, physicalist] scientism is the thesis that the physical world defines reality, that this reality has played out through blind dynamic stochastic forces via cosmological, chemical, biological macro and now sociocultural evolution, where big S science holds monopoly or at least overwhelming superiority on claims to knowledge. This last can reach the notion science is the only begetter of truth, a philosophical claim, so self refuting. of course evolutionary materialism radically undermines credibility of mind as say Haldane pointed out and is also self refuting in many ways. Fellow travellers are accomodationists of one form or another, including many who are religious. I challenge you to show otherwise to be the case ____________ but predict, for cause, you cannot. Fundamentally, it is clear you have no basis to reject that D/RNA includes complex coded algorithms, so language and goal directed — purposeful– procedures; strong signs of design of life from the cell on up through body plans to us. The design inference wins on merits but the establishment will never graciously concede. Revealing, sadly telling. KF

  50. 50
    kairosfocus says:

    PS, for those needing a summary of evo mat scientism, Lewontin’s cat out of the bag moment:

    [Lewontin lets the cat out of the bag:] . . . 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.]

  51. 51
    Sir Giles says:

    KF: SG, predictable turnabout tactic…

    Hmm. How was your rant different than

    Label, assign motivation, polarize, dismiss, rinse, repeat.

  52. 52
    kairosfocus says:

    PPS, The late Philip Johnson’s reply:

    For scientific materialists the materialism comes first; the science comes thereafter. [Emphasis original — the context is Lewontin in NYRB] We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence.

    [–> notice, the power of an undisclosed, question-begging, controlling assumption . . . often put up as if it were a mere reasonable methodological constraint; emphasis added. Let us note how Rational Wiki, so-called, presents it:

    “Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific “dead ends” and God of the gaps-type hypotheses.” [NB: I am aware that Rational Wiki has backed away, un-announced, from the cat-out-of-the-bag direct phrasing that was in place a few years ago. That historic phrasing is still valid as a summary of what is going on.]

    Of course, this ideological imposition on science that subverts it from freely seeking the empirically, observationally anchored truth about our world pivots on the deception of side-stepping the obvious fact since Plato in The Laws Bk X, that there is a second, readily empirically testable and observable alternative to “natural vs [the suspect] supernatural.” Namely, blind chance and/or mechanical necessity [= the natural] vs the ART-ificial, the latter acting by evident intelligently directed configuration. [Cf Plantinga’s reply here and here.]

    And as for the god of the gaps canard, the issue is, inference to best explanation across competing live option candidates. If chance and necessity is a candidate, so is intelligence acting by art through design. And it is not an appeal to ever- diminishing- ignorance to point out that design, rooted in intelligent action, routinely configures systems exhibiting functionally specific, often fine tuned complex organisation and associated information. Nor, that it is the only observed cause of such, nor that the search challenge of our observed cosmos makes it maximally implausible that blind chance and/or mechanical necessity can account for such.]

    That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.”

    . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [Emphasis added.] [The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

  53. 53
    kairosfocus says:

    SG, you know who is addressing and who is evading substance. Evolutionary materialstic scientism and/or fellow travellers, is a substantial summary of a dominant school of thought and its accommodationists, as you full well know. It is not a prejudicially loaded, empty namecalling label, as you also know. I have given reasons for that summary in outline, and just for further point, I now go to roots, 2360 years ago. KF

    PS, Plato warned our civilisation in advance:

    Ath[enian Stranger, in The Laws, Bk X 2,360 ya]. . . .[The avant garde philosophers and poets, c. 360 BC] say that fire and water, and earth and air [i.e the classical “material” elements of the cosmos — the natural order], all exist by nature and chance, and none of them by art . . . [such that] all that is in the heaven, as well as animals and all plants, and all the seasons come from these elements, not by the action of mind, as they say, or of any God, or from art, but as I was saying, by nature and chance only [ –> that is, evolutionary materialism is ancient and would trace all things to blind chance and mechanical necessity; observe, too, the trichotomy: “nature” (here, mechanical, blind necessity), “chance” (similar to a tossed fair die), ART (the action of a mind, i.e. intelligently directed configuration)] . . . .

    [Thus, they hold] that the principles of justice have no existence at all[–> notice the reduction to zero] in nature, but that mankind are always disputing about them and altering them; and that the alterations which are made by art and by law have no basis in nature, but are of authority for the moment and at the time at which they are made.-

    [ –> Relativism, too, is not new; complete with its radical amorality rooted in a worldview that has no foundational IS that can ground OUGHT, leading to an effectively arbitrary foundation only for morality, ethics, so too justice, law and government: accident of personal preference, the ebbs and flows of power politics, accidents of history and and the shifting sands of manipulated community opinion driven by “winds and waves of doctrine and the cunning craftiness of men in their deceitful scheming . . . ” cf a video on Plato’s parable of the cave; from the perspective of pondering who set up the manipulative shadow-shows, why.]

    These, my friends, are the sayings of wise men, poets and prose writers, which find a way into the minds of youth. They are told by them that the highest right is might,

    [ –> Evolutionary materialism — having no IS that can properly ground OUGHT — leads to the promotion of amorality on which the only basis for “OUGHT” is seen to be might (and manipulation: might in “spin”), opening the door to cynicism, hyperskepticism and nihilism . . . this is actually an infamous credo of nihilism . . . also, it reeks of cynically manipulative lawless oligarchy . . . ]

    and in this way the young fall into impieties, under the idea that the Gods are not such as the law bids them imagine; and hence arise factions [ –> Evolutionary materialism-motivated amorality “naturally” leads to continual contentions and power struggles influenced by that amorality at the hands of ruthless power hungry nihilistic agendas], these philosophers inviting them to lead a true life according to nature, that is,to live in real dominion over others [ –> such amoral and/or nihilistic factions, if they gain power, “naturally” tend towards ruthless abuse and arbitrariness . . . they have not learned the habits nor accepted the principles of mutual respect, justice, fairness and keeping the civil peace of justice, so they will want to deceive, manipulate and crush — as the consistent history of radical revolutions over the past 250 years so plainly shows again and again], and not in legal subjection to them [–> nihilistic will to power not the spirit of justice and lawfulness].

  54. 54
    Sir Giles says:

    KF: SG, you know who is addressing and who is evading substance.

    Yup. I am pretty sure it is clear to everyone.

  55. 55
    kairosfocus says:

    SG, you provide an ironic example by way of inviting projective turnabout, MEANWHILE YOU GIVE UTTERLY NO SUBSTANTIAL CONTRIBUTION. That’s a telling clue. Pray, thee, tell us a good reason where there is no good reason to conclude that there are coded algorithms in D/RNA in the cell. Pray, tell us why it is not a reasonable conclusion that we see here language and goal directed processes, signatures of intelligently directed configuration. Tell us, post Lewontin, Crick, Monod, Mahner, NAS and NSTA, et al, that there is no good reason to understand that naturalism often boils down to evolutionary materialistic scientism, and/or that there are not ever so many fellow travellers, and/or that similar views have not haunted our civilisation since Plato in The Laws Bk X. Tell us, pray, that this has not been the main energiser of opposition to the design inference and associated design theory. Answer, predictably, you cannot substantially and accurately do so for facts are readily adduced to show that these are so. The conclusion therefore is, we here see the puff of squid ink to retreat behind tactic. KF

  56. 56
    Sandy says:

    Kairosfocus I think the function argument instead of the code argument is more convincing with people who reject code argument for ideological conviction. They could play stupid games saying they can’t see the code but they can’t do that with function( that is in fact the execution of a code that do not exists 🙂 )

  57. 57
    Alan Fox says:

    Kairosfocus I think the function argument instead of the code argument is more convincing with people who reject code argument for ideological conviction.

    Indeed. I’d be impressed if someone here could show a non-arbitrary connection between sequences and function in a biological context.

    If course reiterative rounds of reproduction with slight genotype variation producing phenotypic change over time by differential reproduction is one explanation for the otherwise arbitrary connection between sequence and function; between genotype and phenotype. So that is the bar set. Have at it!

  58. 58
    kairosfocus says:

    Sandy, an interesting point, though I have seen denial of function too (often pivoting on you cannot define a function), The reality is, we are in a situation where, as the top of the OP outlines, ideological capture of the academy has broken the knowledge commons. We are therefore left to forge our own responsible path to rebuild a sound knowledge base. Part of that starts with the generally recognised fact that D/RNA in the cell contains copious coded algorithmic information. That points to language and to purpose as algorithms are goal directed. Thus, directly to two strong signs of design. The degree of complexity and functionality to chain AAs towards proteins also involves FSCO/I beyond the 500 – 1,000 bit threshold. But we will see endless hyperskeptical objections because this case goes to the start point of cell based life on earth and points to language using intelligence with coding capability backed by deep knowledge of polymer chemistry. The rhetorical stunts above reflect an attempt to pretend that code is a misnomer rooted in weak analogies, that is why I went to a key source on the point, Lehninger. As you can see, the determined objector will always find some real or imaginary hook to hang objections from. We do need to answer, in the end for record, but it is clear where the weight on merits lies. I am also bringing on board the systems engineering and reverse engineering perspective as I think this helps us clarify how we identify structures, patterns and organisation in systems such as the cell. KF

  59. 59
    kairosfocus says:

    AF, you know full well that the programmed AA chains formed in the ribosome by executing code in mRNA are used to fold, cluster and function as proteins, implying deep knowledge of polymer chemistry and the system design that frames the cell. There is a clear connexion, what we have is a considerable distancce to go to understand how chaining, folding and function are sufficiently predictable to be used. That is the cell is well in advance of our current state of knowledge. KF

  60. 60
  61. 61
    whistler says:

    @Alan Fox : Could you explain a function (reproduction, respiration, digestion, etc.) only in terms of chemistry?

  62. 62
    Alan Fox says:

    @Alan Fox : Could you explain a function (reproduction, respiration, digestion, etc.) only in terms of chemistry?

    No. Well, chemical respiration is well-understood, perhaps. But neither can anyone else, certainly not any ID proponent. In principle, biological processes supervene on chemical processes which supervene on the physicochemical properties of molecules. What is “only” doing in your question? Do you want to imply that additional processes are involved? Needed? Such as? Be specific.

  63. 63
    Alan Fox says:

    @ Whistler

    The Krebs cycle, also called The Citric Acid Cycle, is central to cell respiration.

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

  64. 64
    bornagain77 says:

    AF: “(o)f course reiterative rounds of reproduction with slight genotype variation producing phenotypic change over time by differential reproduction is one explanation for the otherwise arbitrary connection between sequence and function; between genotype and phenotype. So that is the bar set. Have at it!”

    And yet,

    With a Startling Candor, Oxford Scientist Admits a Gaping Hole in Evolutionary Theory – November 2011
    Excerpt: As of now, we have no good theory of how to read [genetic] networks, how to model them mathematically or how one network meshes with another; worse, we have no obvious experimental lines of investigation for studying these areas. There is a great deal for systems biology to do in order to produce a full explanation of how genotypes generate phenotypes,,,
    http://www.evolutionnews.org/2.....52821.html

    Researchers Ran a Massive Yearlong Experiment to Get Bacteria to Evolve. Guess What Happened? – August 22, 2014
    Excerpt: “the general inability to connect phenotype to genotype in the context of environmental adaptation has been a major failing in the field of evolution.,,,”
    http://www.evolutionnews.org/2.....89231.html

    “Although this theory [neo-Darwinism] can account for the phenomena it concentrates on, namely, variation of traits in populations, it leaves aside a number of other aspects of evolution… Most important, it completely avoids the origination of phenotypic traits and of organismal form. In other words, neo-Darwinism has no theory of the generative.”
    – Gerd B. Muller & Stuart A. Newman – Origination of Organismal Form, p.7

    Not Junk After All—Conclusion – August 29, 2013
    Excerpt: Many scientists have pointed out that the relationship between the genome and the organism — the genotype-phenotype mapping — cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]
    http://www.uncommondescent.com.....onclusion/

    The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology – Bard – 2011
    Excerpt: If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions [6]. The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits [7]: the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation..
    http://www.biosignaling.com/co.....X-9-30.pdf

    Gene previously linked to obesity is unrelated – June 29, 2015
    Excerpt: … in the real world of careful analysis, scientists are just not finding the “genes” that the headline writers need. British geneticist Steve Jones points out that most human traits are influenced by so many genes that there is no likely systematic cause and effect:
    “We know of more than 50 different genes associated with height … That has not percolated into the public mind, as the Google search for “scientists find the gene for” shows. The three letter word for — the gene FOR something — is the most dangerous word in genetics.”
    And the craze is not harmless, he warns. …
    http://www.uncommondescent.com.....unrelated/

    What If (Almost) Every Gene Affects (Almost) Everything? – JUN 16, 2017
    Excerpt: If you told a modern geneticist that a complex trait—whether a physical characteristic like height or weight, or the risk of a disease like cancer or schizophrenia—was the work of just 15 genes, they’d probably laugh. It’s now thought that such traits are the work of thousands of genetic variants, working in concert. The vast majority of them have only tiny effects, but together, they can dramatically shape our bodies and our health. They’re weak individually, but powerful en masse.
    https://www.theatlantic.com/science/archive/2017/06/its-like-all-connected-man/530532/

    Theory Suggests That All Genes Affect Every Complex Trait – June 20, 2018
    Excerpt: Mutations of a single gene are behind sickle cell anemia, for instance, and mutations in another are behind cystic fibrosis.
    But unfortunately for those who like things simple, these conditions are the exceptions. The roots of many traits, from how tall you are to your susceptibility to schizophrenia, are far more tangled. In fact, they may be so complex that almost the entire genome may be involved in some way,,,
    One very early genetic mapping study in 1999 suggested that “a large number of loci (perhaps > than 15)” might contribute to autism risk, recalled Jonathan Pritchard, now a geneticist at Stanford University. “That’s a lot!” he remembered thinking when the paper came out.
    Over the years, however, what scientists might consider “a lot” in this context has quietly inflated. Last June, Pritchard and his Stanford colleagues Evan Boyle and Yang Li (now at the University of Chicago) published a paper about this in Cell that immediately sparked controversy, although it also had many people nodding in cautious agreement. The authors described what they called the “omnigenic” model of complex traits. Drawing on GWAS analyses of three diseases, they concluded that in the cell types that are relevant to a disease, it appears that not 15, not 100, but essentially all genes contribute to the condition. The authors suggested that for some traits, “multiple” loci could mean more than 100,000.
    https://www.quantamagazine.org/omnigenic-model-suggests-that-all-genes-affect-every-complex-trait-20180620/

    In short,, directly contrary to the ‘selfish gene’ concept of Richard Dawkins, that is more of less directly based on Darwin’s own ‘survival of the fittest’ thinking about competition, genes are instead best thought of as existing in a holistic web of mutual interdependence and cooperation.
    Which is, needless to say, the exact polar opposite of being ‘selfish’. (And should, if Darwinism were a science instead of basically being the religion for atheists, count as yet another direct falsification of Darwinism).

  65. 65
    whistler says:

    Could you explain a function (reproduction, respiration, digestion, etc.) only in terms of chemistry?
    Alan Fox: No.

    You admit that the chemistry cannot account for a function.
    You deny the reality of the code that explains a function easily.
    This is a classic case of denial of reality=a subconscious defense mechanism characterized by refusal to acknowledge (or rationalization of) unwanted or unpleasant facts, realities, thoughts, or feelings.
    PS: It’s the same denial of reality of atheists about origins: We don’t know how life emerged but certainly wasn’t God. 🙂

  66. 66
    kairosfocus says:

    AF, have you pondered singing, speaking, the vocal tract, thence words, language and encoded contextually sensitive meanings? Try, Sinach. KF

  67. 67
    Alan Fox says:

    You admit that the chemistry cannot account for a function.

    I admitted no such thing, Oh mischievous mover of goalposts.

    ETA:

    Actual reply:

    @Alan Fox : Could you explain a function (reproduction, respiration, digestion, etc.) only in terms of chemistry?

    No. Well, chemical respiration is well-understood, perhaps. But neither can anyone else, certainly not any ID proponent. In principle, biological processes supervene on chemical processes which supervene on the physicochemical properties of molecules. What is “only” doing in your question? Do you want to imply that additional processes are involved? Needed? Such as? Be specific.

  68. 68
    whistler says:

    Alan Fox

    Whistler
    You admit that the chemistry cannot account for a function.

    I admitted no such thing, Oh mischievous mover of goalposts.

    If you didn’t admit such a thing then certainly you can explain a function only with chemistry but you forgot to explain it.

  69. 69
    Alan Fox says:

    If you didn’t admit such a thing then certainly you can explain a function only with chemistry but you forgot to explain it.

    Still goalpost shifting? I said I couldn’t explain every biological process in complete detail. I did point out the Krebs cycle is well understood. Did you follow my link?

  70. 70
    whistler says:

    Alan Fox
    I said I couldn’t explain every biological process in complete detail. I did point out the Krebs cycle is well understood. Did you follow my link?

    🙂 I asked you to explain how an engine’s function appeared and you tell me how is working . It’s impossible to explain a function only with chemistry because chemistry is just ore while life is like a processor with billions of transistors . The ore doesn’t build the processor and the chemistry doesn’t build life. Something else do it .

  71. 71
    Alan Fox says:

    It’s impossible to explain a function only with chemistry because chemistry is just ore while life is like a processor with billions of transistors.

    That cellular life is chemistry, follows the same rules and patterns of molecular interactions, and is eminently observable is obvious to anyone who is interested enough to give biology at least a cursory look. Sure, our current level of understanding doesn’t allow us a complete overarching understanding of the whole process in every detail but research goes on.

    Whistler’s misunderstandings and misrepresentations matter not at all; the biological sciences will continue as long as they are useful.

  72. 72
    whistler says:

    Alan Fox
    That cellular life is chemistry

    Nonsense. It is not chemistry , it is CONTROLLED chemistry . What controls the chemistry ? Can’t be the chemistry that controls the chemistry, right?

    PS: Again, how chemistry creates a function?

  73. 73
    Alan Fox says:

    What controls the chemistry ? Can’t be the chemistry that controls the chemistry, right?

    Any chemical reaction will proceed until it reaches equilibrium. Add more reactants or remove the products of the reaction and equilibrium is not reached. Biological entities such as cells maintain themselves out of equilibrium but require an energy source to do so. Starve an organism of its energy source and it dies, returns to equilibrium with its surroundings.

    I take it your education did not include biology or chemistry. But it really doesn’t matter if Whistler disagrees that life is chemical. Life ignores Whistler and carries on regardless.

  74. 74
    bornagain77 says:

    Hey, Paul Davies — Your ID Is Showing – Robert F. Shedinger – March 6, 2020
    Excerpt: With a nod toward James Clerk Maxwell’s entropy-defying demon, Davies argues that the gulf between physics and biology is completely unbridgeable without some fundamentally new concept. Since living organisms consistently resist the ravages of entropy that all forms of inanimate matter are subject to, there must be some non-physical principle allowing living matter to consistently defy the Second Law of Thermodynamics. And for Davies there is; the demon in the machine turns out to be information.
    https://evolutionnews.org/2020/03/hey-paul-davies-your-id-is-showing/

    Information and Thermodynamics in Living Systems – Andy C. McIntosh – 2013
    Excerpt: ,,, information is in fact non-material and that the coded information systems (such as, but not restricted to the coding of DNA in all living systems) is not defined at all by the biochemistry or physics of the molecules used to store the data. Rather than matter and energy defining the information sitting on the polymers of life, this approach posits that the reverse is in fact the case. Information has its definition outside the matter and energy on which it sits, and furthermore constrains it to operate in a highly non-equilibrium thermodynamic environment. This proposal resolves the thermodynamic issues and invokes the correct paradigm for understanding the vital area of thermodynamic/organisational interactions, which despite the efforts from alternative paradigms has not given a satisfactory explanation of the way information in systems operates.,,,
    http://www.worldscientific.com.....08728_0008
    Andrew McIntosh (also known as Andy McIntosh) is professor of thermodynamics and combustion theory at the University of Leeds.

    Recognising Top-Down Causation – George Ellis
    Excerpt: Causation: The nature of causation is highly contested territory, and I will take a pragmatic view:
    Definition 1: Causal Effect
    If making a change in a quantity X results in a reliable demonstrable change in a quantity Y in a given context, then X has a causal effect on Y.
    Example: I press the key labelled “A” on my computer keyboard; the letter “A” appears on my computer screen.,,,
    Definition 2: Existence
    If Y is a physical entity made up of ordinary matter, and X is some kind of entity that has a demonstrable causal effect on Y as per Definition 1, then we must acknowledge that X also exists (even if it is not made up of such matter).
    This is clearly a sensible and testable criterion; in the example above, it leads to the conclusion that both the data and the relevant software exist. If we do not adopt this definition, we will have instances of uncaused changes in the world; I presume we wish to avoid that situation.,,,
    ,,,However there are many topics that one cannot understand by assuming this one-way flow of causation. The flourishing subject of social neuroscience makes clear how social influences act down on individual brain structure[2]; studies in physiology demonstrate that downward causation is necessary in understanding the heart, where this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes[3]; epigenetic studies demonstrate that biological development is crucially shaped by the environment[4]
    What about physics? In this essay I will make the case that top-down causation is also prevalent in physics, even though this is not often recognised as such. This does not occur by violating physical laws; on the contrary, it occurs through the laws of physics, by setting constraints on lower level interactions.
    Excerpt: page 5: A:
    Both the program and the data are non-physical entities, indeed so is all software. A program is not a physical thing you can point to, but by Definition 2 it certainly exists. You can point to a CD or flashdrive where it is stored, but that is not the thing in itself: it is a medium in which it is stored.
    The program itself is an abstract entity, shaped by abstract logic. Is the software “nothing but” its realisation through a specific set of stored electronic states in the computer memory banks? No it is not because it is the precise pattern in those states that matters: a higher level relation that is not apparent at the scale of the electrons themselves. It’s a relational thing (and if you get the relations between the symbols wrong, so you have a syntax error, it will all come to a grinding halt). This abstract nature of software is realised in the concept of virtual machines, which occur at every level in the computer hierarchy except the bottom one [17]. But this tower of virtual machines causes physical effects in the real world, for example when a computer controls a robot in an assembly line to create physical artefacts.
    Excerpt page 7: The assumption that causation is bottom up only is wrong in biology, in computers, and even in many cases in physics, for example state vector preparation, where top-down constraints allow non-unitary behaviour at the lower levels. It may well play a key role in the quantum measurement problem (the dual of state vector preparation) [5]. One can bear in mind here that wherever equivalence classes of entities play a key role, such as in Crutchfield’s computational mechanics [29], this is an indication that top-down causation is at play.,,,
    Life and the brain: living systems are highly structured modular hierarchical systems, and there are many similarities to the digital computer case, even though they are not digital computers. The lower level interactions are constrained by network connections, thereby creating possibilities of truly complex behaviour. Top-down causation is prevalent at all levels in the brain: for example it is crucial to vision [24,25] as well as the relation of the individual brain to society [2]. The hardware (the brain) can do nothing without the excitations that animate it: indeed this is the difference between life and death. The mind is not a physical entity, but it certainly is causally effective: proof is the existence of the computer on which you are reading this text. It could not exist if it had not been designed and manufactured according to someone’s plans, thereby proving the causal efficacy of thoughts, which like computer programs and data are not physical entities.
    https://arxiv.org/pdf/1212.2275.pdf

    The Unbearable Wholeness of Beings – Stephen L. Talbott – 2010
    Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary.
    ,,, the question, rather, is why things don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer?
    Despite the countless processes going on in the cell, and despite the fact that each process might be expected to “go its own way” according to the myriad factors impinging on it from all directions, the actual result is quite different. Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity.
    http://www.thenewatlantis.com/.....-of-beings

  75. 75
    whistler says:

    Alan Fox
    Any chemical reaction will proceed until it reaches equilibrium.

    🙂 Nobody asked you to describe how proceed a chemical reaction but what directs and allow a very specific chemical reaction -not “any” random possible chemical reaction – to take place in what specific area of the cell( or organelles) for what specific purpose? Do you have understanding problems or is just a (useless) tactic to avoid humiliation?

  76. 76
    Alan Fox says:

    what directs and allow a very specific chemical reaction -not “any” random possible chemical reaction – to take place in what specific area of the cell ( or organelles) for what specific purpose?

    Nothing directs. The chemistry in a cell is precisely the same as in vitro. There’s no élan vital.

  77. 77
    Alan Fox says:

    Chemical reactions are not random. Mix hydrogen and oxygen and add a spark and, without direction, two atoms of hydrogen will combine with one atom of oxygen to form one molecule of water.

  78. 78
    jerry says:

    Nothing directs

    But there might be forces/variables that affect whether a chemical reaction takes place or not or which of the millions takes place.

    From what I understand there is an immense number of factors that affects what happens in a cell. And many are unknown. Where did all these factors come from?

    I believe there are millions of reactions taking place every second in each cell. The proportion of the myriad reactions differs from moment to moment and form cell to cell.

    Since we have trillions of cells, the coordination of these reactions remains a mystery not only in what they are but how they arose and what controls them. Yes, a major mystery.

    How many reactions? Quintillions per second?

    This discussion should be taking place on an origin of life thread. But distractions are the rule not focus.

  79. 79
    bornagain77 says:

    Whistler asks, “what directs and allow a very specific chemical reaction -not “any” random possible chemical reaction – to take place in what specific area of the cell( or organelles) for what specific purpose?”

    AF responds, “Nothing directs. The chemistry in a cell is precisely the same as in vitro. There’s no élan vital.”

    So, according to AF, nothing in the cell is directing specific chemical reactions to occur in a specific place, at a specific time, and for a specific purpose? Really???

    That claim doesn’t even pass the smell test.

    And AF accused Whistler of being ignorant for not believing, as AF does, that “life is chemical”?

    Passing the baton of life – from Schrödinger to (Craig) Venter – July 2012
    Excerpt: “All living cells that we know of on this planet are ‘DNA software’-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions,” said Venter. “We are now using computer software to design new DNA software.”
    The digital and biological worlds are becoming interchangeable, he added, describing how scientists now simply send each other the information to make DIY biological material rather than sending the material itself.
    Venter also outlined a vision of small converter devices that can be attached to computers to make the structures from the digital information,,,
    https://newsworldofscience.blogspot.com/2012/07/passing-baton-of-life-from-schrodinger.html

    Programming of Life – Don Johnson – video
    https://www.youtube.com/watch?v=00vBqYDBW5s
    * in each cell, there are multiple operating systems, multiple programming languages, encoding/decoding hardware and software, specialized communications systems, error detection/correction systems, specialized input/output for organelle control and feedback, and a variety of specialized “devices” to accomplish the tasks of life.

    Cells Are Like Robust Computational Systems, – June 2009
    Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,”We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail.”
    http://www.sciencedaily.com/re.....103205.htm

    Systems biology: Untangling the protein web – July 2009
    Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. “Combine all this and you can start to think that maybe some of the information flow can be captured,” he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. “The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent,” he says. “The simple pathway models are a gross oversimplification of what is actually happening.”
    http://www.nature.com/nature/j.....0415a.html

  80. 80
    relatd says:

    Ba77,

    All of this proven complexity, yet the ‘usual suspects’ like AF, CD, Seversky and a few others will ALWAYS deflect, deny and make it more simple than it really is. Sad.

  81. 81
    kairosfocus says:

    AF, you are blind to systems architecture on this topic as acknowledging that it is real would be fatal to your preferred views. Yes, there is a physical layer using polymer chemistry based nanotech. There is a digital layer in the mRNA, using coded algorithms to sequence AA chains that then are folded etc to form functional proteins. That speaks to deep understanding of the chem but also to the digital layer using codes and algorithms. Which for weeks now you have been desperate to deny and dismiss. Even when corrected by leading authorities in the field you tried to use, to give plausibility to your denial tactics, biochem. Yes, the said authorities then go on to postulate an utterly implausible spontaneous process to get to that architecture. That is unsurprising goiven current circumstances. But that does not change the force of what has been learned since the 1950’s about protein synthesis. KF

  82. 82
    bornagain77 says:

    As to AF’s appeal to ‘simple’ water to try to support his atheistic worldview, i.e. “two atoms of hydrogen will combine with one atom of oxygen to form one molecule of water.”

    It turns out that even something as simple as water refutes AF’s atheistic worldview,

    Water, Ultimate Giver of Life, Points to Intelligent Design – (Michael Denton 2017) video
    https://www.youtube.com/watch?v=e2i0g1sL-X4

    Pro-Intelligent Design Peer Reviewed Scientific Paper Argues for an “Engineered World”
    Casey Luskin – December 26, 2010
    Excerpt: Another aspect of the universe they claim shows evidence of engineering is its “biofriendliness.” They focus on the life-sustaining properties of water:
    “The remarkable properties of water are numerous. Its very high specific heat maintains relatively stable temperatures both in oceans and organisms. As a liquid, its thermal conductivity is four times any other common liquid, which makes it possible for cells to efficiently distribute heat. On the other hand, ice has a low thermal conductivity, making it a good thermal shield in high latitudes. A latent heat of fusion only surpassed by that of ammonia tends to keep water in liquid form and creates a natural thermostat at 0°C. Likewise, the highest latent heat of vaporization of any substance – more than five times the energy required to heat the same amount of water from 0°C-100°C – allows water vapor to store large amounts of heat in the atmosphere. This very high latent heat of vaporization is also vital biologically because at body temperature or above, the only way for a person to dissipate heat is to sweat it off.
    Water’s remarkable capabilities are definitely not only thermal. A high vapor tension allows air to hold more moisture, which enables precipitation. Water’s great surface tension is necessary for good capillary effect for tall plants, and it allows soil to hold more water. Water’s low viscosity makes it possible for blood to flow through small capillaries. A very well documented anomaly is that water expands into the solid state, which keeps ice on the surface of the oceans instead of accumulating on the ocean floor. Possibly the most important trait of water is its unrivaled solvency abilities, which allow it to transport great amounts of minerals to immobile organisms and also hold all of the contents of blood. It is also only mildly reactive, which keeps it from harmfully reacting as it dissolves substances. Recent research has revealed how water acts as an efficient lubricator in many biological systems from snails to human digestion. By itself, water is not very effective in this role, but it works well with certain additives, such as some glycoproteins. The sum of these traits makes water an ideal medium for life. Literally, every property of water is suited for supporting life. It is no wonder why liquid water is the first requirement in the search for extraterrestrial intelligence.
    All these traits are contained in a simple molecule of only three atoms. One of the most difficult tasks for an engineer is to design for multiple criteria at once. … Satisfying all these criteria in one simple design is an engineering marvel. Also, the design process goes very deep since many characteristics would necessarily be changed if one were to alter fundamental physical properties such as the strong nuclear force or the size of the electron.”
    They then explore why the very elements that are most common in life — hydrogen, carbon, and oxygen — are so prevalent in the universe:
    “Hydrogen, oxygen, and carbon rank one, three, and four, respectively, in prevalence in the universe (helium is the other). The explanation has to do with fusion within stars. Early reactions start with hydrogen atoms and then produce deuterium (mass 2), tritium (mass 3), and alpha particles (mass 4), but no stable mass 5 exists. This limits the creation of heavy elements and was considered one of “God’s mistakes” until further investigation. In actuality, the lack of a stable mass 5 necessitates bigger jumps of four which lead to carbon (mass 12) and oxygen (mass 16). Otherwise, the reactions would have climbed right up the periodic table in mass steps of one (until iron, which is the cutoff above which fusion requires energy rather than creating it). The process would have left oxygen and carbon no more abundant than any other element.”
    The authors then quote Fred Hoyle on the subject, who stated, “I do not believe that any scientist who examined the evidence would fail to draw the inference that the laws of nuclear physics have been deliberately designed with regard to the consequences they produce inside the stars.”
    https://evolutionnews.org/2010/12/pro-intelligent_design_peer_re/

    Water’s quantum weirdness makes life possible – October 2011
    Excerpt: WATER’S life-giving properties exist on a knife-edge. It turns out that life as we know it relies on a fortuitous, but incredibly delicate, balance of quantum forces.,,,
    They found that the hydrogen-oxygen bonds were slightly longer than the deuterium-oxygen ones, which is what you would expect if quantum uncertainty was affecting water’s structure. “No one has ever really measured that before,” says Benmore.
    We are used to the idea that the cosmos’s physical constants are fine-tuned for life. Now it seems water’s quantum forces can be added to this “just right” list.
    http://www.newscientist.com/ar.....sible.html

    Water Is ‘Designer Fluid’ That Helps Proteins Change Shape – 2008
    Excerpt: “When bound to proteins, water molecules participate in a carefully choreographed ballet that permits the proteins to fold into their functional, native states. This delicate dance is essential to life.”
    http://www.sciencedaily.com/re.....113314.htm

  83. 83
    Alan Fox says:

    BA77,

    You overlooked the amazing properties of the hydrogen bond that results in some of water’s unique properties as an almost universal solvent and how the hydrogen bond is central to base pairing in DNA and RNA.

  84. 84
    bornagain77 says:

    DNA is held together by hydrophobic forces – SEPTEMBER 23, 2019
    Excerpt: Researchers at Chalmers University of Technology, Sweden, have disproved the prevailing theory of how DNA binds itself. It is not, as is generally believed, hydrogen bonds which bind together the two sides of the DNA structure. Instead, water is the key. The discovery opens doors for new understanding in research in medicine and life sciences. The findings are published in PNAS.
    DNA is constructed of two strands consisting of sugar molecules and phosphate groups. Between these two strands are nitrogen bases, the compounds that make up genes, with hydrogen bonds between them. Until now, it was commonly thought that those hydrogen bonds held the two strands together.
    But now, researchers from Chalmers University of Technology show that the secret to DNA’s helical structure may be that the molecules have a hydrophobic interior, in an environment consisting mainly of water. The environment is therefore hydrophilic, while the DNA molecules’ nitrogen bases are hydrophobic, pushing away the surrounding water. When hydrophobic units are in a hydrophilic environment, they group together to minimize their exposure to the water.
    The role of the hydrogen bonds, which were previously seen as crucial to holding DNA helixes together, appear to be more to do with sorting the base pairs so that they link together in the correct sequence. The discovery is crucial for understanding DNA’s relationship with its environment.
    “Cells want to protect their DNA, and not expose it to hydrophobic environments, which can sometimes contain harmful molecules,” says Bobo Feng, one of the researchers behind the study. “But at the same time, the cells’ DNA needs to open up in order to be used.”
    “We believe that the cell keeps its DNA in a water solution most of the time, but as soon as a cell wants to do something with its DNA, like read, copy or repair it, it exposes the DNA to a hydrophobic environment.”
    Reproduction, for example, involves the base pairs dissolving from one another and opening up. Enzymes then copy both sides of the helix to create new DNA. When it comes to repairing damaged DNA, the damaged areas are subjected to a hydrophobic environment, to be replaced. A catalytic protein creates the hydrophobic environment. This type of protein is central to all DNA repairs, meaning it could be the key to fighting many serious sicknesses.,,,
    The researchers observed that when the solution reached the borderline between hydrophilic and hydrophobic, the DNA molecules’ characteristic spiral form started to unravel.
    Upon closer inspection, they observed that when the base pairs split from one another (due to external influence, or simply from random movements), holes are formed in the structure, allowing water to leak in. Because DNA wants to keep its interior dry, it presses together, with the base pairs coming together again to squeeze out the water. In a hydrophobic environment, this water is missing, so the holes stay in place.
    https://phys.org/news/2019-09-dna-held-hydrophobic.html

  85. 85
    Alan Fox says:

    BTW BA77
    My original mention of water was to refute someone’s assertion that chemistry is random by pointing out that water molecules always consist of one atom of oxygen linked to two atoms of hydrogen, with paired electrons spending more time (probably – but the probability is eminently predictable and non-random) nearer the oxygen nucleus. This is the key that allows hydrogen bonds to form and explains the non-linear shape of water molecules.

  86. 86
    Alan Fox says:

    PS, it also explains how water in a puddle so perfectly fills the hole.

  87. 87
    bornagain77 says:

    And my point was to point out that something as ‘simple’ as water refutes the atheistic worldview and supports Intelligent Design. Funny how that works eh?

    Also see,

    Privileged Species – How the cosmos is designed for human life – video (2015) (13:29 minute mark; water’s thermal properties, 15:00 minute mark; evaporative cooling is optimal for humans in particular)
    https://youtu.be/VoI2ms5UHWg?t=809

    The Miracle of Man: Extraordinary “Coincidences” All the Way Down –
    – June 9, 2022
    Excerpt: On a new episode of ID the Future, Miracle of Man author and biologist Michael Denton continues his conversation with host Eric Anderson. Here Denton offers a review of several more anthropic “coincidences” in chemistry, biochemistry, and Earth sciences that are fine tuned to allow air-breathing, bipedal, technology-developing terrestrial creatures like ourselves to exist and thrive. The fine tuning, what Denton calls anthropic prior fitness, would seem to require foresight and planning on literally a cosmic scale.
    https://evolutionnews.org/2022/06/the-miracle-of-man-extraordinary-coincidences-all-the-way-down/
    First three parts of the interview with Dr. Denton are here
    1
    https://idthefuture.com/1601/
    2
    https://idthefuture.com/1604/
    3
    https://idthefuture.com/1606/

    The Miracle of Man: The Fine Tuning of Nature for Human Existence (Privileged Species Series) – May 6, 2022
    https://www.amazon.com/dp/1637120125/

  88. 88
    Alan Fox says:

    And my point was to point out that something as ‘simple’ as water refutes the atheistic worldview and supports Intelligent Design.

    But you are wrong. Water is not simple. And I’ve never heard the argument that because water is simple , God doesn’t exist. That is a completely mad non-sequitur.

  89. 89
    Alan Fox says:

    I mean it would be equally daft to say water is not simple, therefore God. Surely nobody makes such a silly argument?

    Do they?

  90. 90
    bornagain77 says:

    “Do they?” 🙂

    That seems to have been asked with a bit of nervousness. 🙂

    But alas, (since we are indeed made in the ‘image of God’), the design intuition in humans runs very deep and it is only by purposely suppressing their innate design inference that atheists, such as yourself, can maintain their atheistic worldview against all evidence to the contrary.

    Is Atheism a Delusion?
    https://www.youtube.com/watch?v=_Ii-bsrHB0o

    Design Thinking Is Hardwired in the Human Brain. How Come? – October 17, 2012
    Excerpt: “Even Professional Scientists Are Compelled to See Purpose in Nature, Psychologists Find.” The article describes a test by Boston University’s psychology department, in which researchers found that “despite years of scientific training, even professional chemists, geologists, and physicists from major universities such as Harvard, MIT, and Yale cannot escape a deep-seated belief that natural phenomena exist for a purpose” ,,,
    Most interesting, though, are the questions begged by this research. One is whether it is even possible to purge teleology from explanation.
    http://www.evolutionnews.org/2.....65381.html

    Richard Dawkins take heed: Even atheists instinctively believe in a creator says study – Mary Papenfuss – June 12, 2015
    Excerpt: Three studies at Boston University found that even among atheists, the “knee jerk” reaction to natural phenomenon is the belief that they’re purposefully designed by some intelligence, according to a report on the research in Cognition entitled the “Divided Mind of a disbeliever.”
    The findings “suggest that there is a deeply rooted natural tendency to view nature as designed,” writes a research team led by Elisa Järnefelt of Newman University. They also provide evidence that, in the researchers’ words, “religious non-belief is cognitively effortful.”
    Researchers attempted to plug into the automatic or “default” human brain by showing subjects images of natural landscapes and things made by human beings, then requiring lightning-fast responses to the question on whether “any being purposefully made the thing in the picture,” notes Pacific-Standard.
    “Religious participants’ baseline tendency to endorse nature as purposefully created was higher” than that of atheists, the study found. But non-religious participants “increasingly defaulted to understanding natural phenomena as purposefully made” when “they did not have time to censor their thinking,” wrote the researchers.
    The results suggest that “the tendency to construe both living and non-living nature as intentionally made derives from automatic cognitive processes, not just practised explicit beliefs,” the report concluded.
    The results were similar even among subjects from Finland, where atheism is not a controversial issue as it can be in the US.
    “Design-based intuitions run deep,” the researchers conclude, “persisting even in those with no explicit religious commitment and, indeed, even among those with an active aversion to them.”
    http://www.ibtimes.co.uk/richa.....dy-1505712

    Perhaps the two most famous quotes of atheists suppressing their innate ‘design inference’ are the two following quotes:

    “Yet the living results of natural selection overwhelmingly impress us with the appearance of design as if by a master watchmaker, impress us with the illusion of design and planning.”
    Richard Dawkins – “The Blind Watchmaker” – 1986 – page 21

    “Biologists must constantly keep in mind that what they see was not designed, but rather evolved. It might be thought, therefore, that evolutionary arguments would play a large part in guiding biological research, but this is far from the case”
    – Francis Crick – What Mad Pursuit – 1988

    It is very easy to see why Francis Crick in particular, co-discoverer of the DNA helix, would be constantly haunted by his innate belief that life must be Intelligently Designed. DNA itself literally screams, “I AM INTELLIGENTLY DESIGNED” from every angle that you look at it.
    Jan 2022
    https://uncommondescent.com/intelligent-design/movie-night-with-illustra-a-whale-of-a-story-and-18-trillion-feet-of-you/#comment-745611

    Romans 1:19-20
    For what can be known about God is plain to them, because God has shown it to them. For his invisible attributes, namely, his eternal power and divine nature, have been clearly perceived, ever since the creation of the world, in the things that have been made. So they are without excuse.

  91. 91
    Alan Fox says:

    The simpleness or otherwise of water is not mentioned. Try again, Phil.

  92. 92
    bornagain77 says:

    Whatever AF. Denial is NOT a river in Egypt.

    Hear no Intelligent Design, See no Intelligent Design, Speak no Intelligent Design.
    https://i.pinimg.com/originals/a7/5a/33/a75a33e0054eac9a2ecdf69f735b8104.jpg

    In the psychology of human behavior, denialism is a person’s choice to deny reality, as a way to avoid a psychologically uncomfortable truth.
    – Denialism – Wikipedia

  93. 93
    Alan Fox says:

    Phil, you first told me water isn’t simple, with which statement I agree, then you told me that people argue that water being not simple is an argument for God, which is a non-sequitur, but have not produced a single example. Then you tell me that atheists claim the simplicity of water proves the non-existence of God, which would be a daft argument. No examples from you. All the while claiming I am an atheist. I’m certainly not a Christian but I haven’t ruled out other possibilities. I accept the description of agnostic.

    So who’s the denier here, Phil?

  94. 94
    relatd says:

    Denial is not a river in Egypt? Huh… huh. After all this time…

  95. 95
    bornagain77 says:

    So AF does not deny God per se, he just denies that anything in the universe, like water, and/or a cell, can be evidence for Intelligent Design.. Gotcha buddy.,,, Let’s just call it ‘selective denialism for rhetorical purposes’ shall we? 🙂

  96. 96
    Alan Fox says:

    So AF does not deny God per se, he just denies that anything in the universe, like water, and/or a cell, can be evidence for Intelligent Design.

    Lets’s be clear. It is very simplistic to argue the universe is either the result of physical processes or due to divine intervention. Neither position is defensible. There is no empirical explanation [oops pressed post in error] for the origin of this universe or the origin of life on Earth. Nor is there any evidenced consensual religious explanation. Nobody knows, though many are full of ideas.

  97. 97
    bornagain77 says:

    ^^^ LOL,

    And right on cue, AF gives a shining example of denialism.

    You simply can’t make this stuff up, nobody would believe it. 🙂

    LOL, thanks for playing.

  98. 98
    Alan Fox says:

    Naughty Phil. Others can read for themselves. Actually, I have to say the relaxed moderation here is a refreshing change from earlier times.

  99. 99
    Alan Fox says:

    I mean, remember the times when you would call on the voice in the ceiling to ban someone and, hey presto, they would disappear? It’s so much better now, wouldn’t you agree?

  100. 100
    bornagain77 says:

    Yes I agree, the new policy of “give enough rope to a Darwinian atheist and he will hang himself” seems to working out quite well. 🙂
    https://st.depositphotos.com/1009764/2328/i/950/depositphotos_23286678-stock-photo-hanging-man.jpg

  101. 101
    Alan Fox says:

    May not surprise you to know that the hubristic poses if some reconstructionists, fundamentalists and right-wing evangelicals give Jesus’ published teachings a bad name, in my view.

  102. 102
    kairosfocus says:

    AF, you have kept 3 mm on the side of the line, showing you know where it is. KF

  103. 103
    kairosfocus says:

    AF, BTW, equally, you know the issue is origin of the system architecture of the universe which shows fine tuning, likewise origin of life using complex coded algorithms. But of course you seemingly cannot resist setting up and knocking over strawman caricatures. Showing, that you have no substantial answer on the merits. Duly noted. KF

  104. 104
    Sir Giles says:

    AF: PS, it also explains how water in a puddle so perfectly fills the hole.

    It’s almost as if the hole was designed and finely tuned for the benefit of the puddle.

  105. 105
    bornagain77 says:

    The Trouble with “Puddle Thinking”: A User’s Guide to the Anthropic Principle – Geraint F. Lewis, Luke A. Barnes – June 2021
    https://arxiv.org/abs/2104.03381

    Does the Puddle Analogy Explain Cosmic Fine-Tuning? by Hugh Ross – June 7, 2021
    Excerpt: Problems with “Puddle Thinking”
    A few weeks ago, Australian astronomers Geraint Lewis and Luke Barnes published what, in my opinion, is the most eloquent and lay-accessible rebuttal to the puddle argument.5 They begin by giving the puddle the name Doug. Doug the puddle observes an exact match between his shape and the shape of the hole in which he dwells. Doug concludes that Someone must have designed the hole just for him. What Doug fails to realize is that given the fluidity of the water, the solidity of the hole, and the force of gravity, he will always take on the identical shape of his hole. Lewis and Barnes point out the obvious: any hole will do for a puddle.
    The puddle analogy for humanity’s existence in the universe is fatally flawed. The two astronomers explain that not every conceivable universe will do for physical life. Physical life is not like a fluid. It will not and cannot adjust to any universe. The fine-tuning that astronomers observe indicates that even very slight alterations to the universe’s characteristics would rule out the possible existence of physical life. For human life, and especially for global human civilization, the constraints on the universe’s characteristics are exponentially more fine-tuned.,,,
    Lewis and Barnes conclude that the fallacies in the puddle argument imply that the cosmic fine-tuning that astronomers observe cannot be dismissed as unworthy of our attention.,,,
    https://reasons.org/explore/blogs/todays-new-reason-to-believe/does-the-puddle-analogy-explain-cosmic-fine-tuning

  106. 106
    Sir Giles says:

    BA77: The Trouble with “Puddle Thinking”

    The trouble with “Puddle Thinking” is those who think they have to respond to “Puddle Thinking”. In the famous words of of the Bard “The lady doth protest too much, methinks”.

  107. 107
    bornagain77 says:

    The Trouble with Puddle Thinking – Alas Lewis & Barnes
    https://www.youtube.com/watch?v=2-AIItNLTDw

  108. 108
    bornagain77 says:

    A Reasonable Little Question: A Formulation of the Fine-Tuning Argument – Barnes – 2020
    A new formulation of the Fine-Tuning Argument (FTA) for the existence of God is offered, which avoids a number of commonly raised objections. I argue that we can and should focus on the fundamental constants and initial conditions of the universe, and show how physics itself provides the probabilities that are needed by the argument. I explain how this formulation avoids a number of common objections, specifically the possibility of deeper physical laws, the multiverse, normalisability, whether God would fine-tune at all, whether the universe is too fine-tuned, and whether the likelihood of God creating a life-permitting universe is inscrutable.
    Is the physical world all that exists? Are the ultimate laws of the physical universe the end of all explanations, or is there something about our universe that is noteworthy or rare or clever or unexpected?
    https://theisticscience.com/papers/tree/VariableCouplings/Barnes-Ergo2020-reasonable-little-question-a-formulation-of-the-fine-tuning.pdf
    Extremely long. But,,
    5. Conclusion
    What physical universe would we expect to exist, if naturalism were true? To systematically and tractably explore other ways that the universe could have been, we vary the free parameters of the standard models of particle physics and cosmology. This exercise could have discovered that our universe is typical and unexceptional. It did not. This search for other ways that the universe could have been has overwhelmingly found lifelessness.
    In short, the answer to the Little Question is no. And so, plausibly and as best we can tell, the answer to the Big Question is no. The fine-tuning of the universe for life shows that, according to the best physical theories we have, naturalism overwhelmingly expects a dead universe.

    The Fine-Tuning of Nature’s Laws – Luke A. Barnes – Fall 2015
    Excerpt: Today, our deepest understanding of the laws of nature is summarized in a set of equations. Using these equations, we can make very precise calculations of the most elementary physical phenomena, calculations that are confirmed by experimental evidence. But to make these predictions, we have to plug in some numbers that cannot themselves be calculated but are derived from measurements of some of the most basic features of the physical universe. These numbers specify such crucial quantities as the masses of fundamental particles and the strengths of their mutual interactions. After extensive experiments under all manner of conditions, physicists have found that these numbers appear not to change in different times and places, so they are called the fundamental constants of nature.
    These constants represent the edge of our knowledge. Richard Feynman called one of them — the fine-structure constant, which characterizes the amount of electromagnetic force between charged elementary particles like electrons — “one of the greatest damn mysteries of physics: a magic number that comes to us with no understanding by man.” An innovative, elegant physical theory that actually predicts the values of these constants would be among the greatest achievements of twenty-first-century physics.
    Many have tried and failed. ,,,
    Tweaking the Constants
    Let’s consider a few examples of the many and varied consequences of messing with the fundamental constants of nature, the initial conditions of the universe, and the mathematical form of the laws themselves.
    You are made of cells; cells are made of molecules; molecules of atoms; and atoms of protons, neutrons, and electrons. Protons and neutrons, in turn, are made of quarks. We have not seen any evidence that electrons and quarks are made of anything more fundamental (though other fundamental particles, like the Higgs boson of recent fame, have also been discovered in addition to quarks and electrons). The results of all our investigations into the fundamental building blocks of matter and energy are summarized in the Standard Model of particle physics, which is essentially one long, imposing equation. Within this equation, there are twenty-six constants, describing the masses of the fifteen fundamental particles, along with values needed for calculating the forces between them, and a few others. We have measured the mass of an electron to be about 9.1 x 10^-28 grams, which is really very small — if each electron in an apple weighed as much as a grain of sand, the apple would weigh more than Mount Everest. The other two fundamental constituents of atoms, the up and down quarks, are a bit bigger, coming in at 4.1 x 10^-27 and 8.6 x 10^-27 grams, respectively. These numbers, relative to each other and to the other constants of the Standard Model, are a mystery to physics. Like the fine-structure constant, we don’t know why they are what they are.
    However, we can calculate all the ways the universe could be disastrously ill-suited for life if the masses of these particles were different. For example, if the down quark’s mass were 2.6 x 10^-26 grams or more, then adios, periodic table! There would be just one chemical element and no chemical compounds, in stark contrast to the approximately 60 million known chemical compounds in our universe.
    With even smaller adjustments to these masses, we can make universes in which the only stable element is hydrogen-like. Once again, kiss your chemistry textbook goodbye, as we would be left with one type of atom and one chemical reaction. If the up quark weighed 2.4 x 10^-26 grams, things would be even worse — a universe of only neutrons, with no elements, no atoms, and no chemistry whatsoever.
    ,,, Compared to the range of possible masses that the particles described by the Standard Model could have, the range that avoids these kinds of complexity-obliterating disasters is extremely small. Imagine a huge chalkboard, with each point on the board representing a possible value for the up and down quark masses. If we wanted to color the parts of the board that support the chemistry that underpins life, and have our handiwork visible to the human eye, the chalkboard would have to be about ten light years (a hundred trillion kilometers) high.,,,
    http://www.thenewatlantis.com/.....tures-laws

  109. 109
    kairosfocus says:

    SG, it is obvious you are not examining the substantial issue, just setting up an inept simplistic strawman and talking as though it dismisses the substantial case. This again underscores just how insubstantial the objecting case is and how much it is driven by ideology. For just one example, a puddle argument stretched to be something substantial implies fine tuning is mechanical necessity like gravity and water settling in holes. That’s a super law argument. However, such a super law would be exquisitely fine tuned to the point we could give it one of those titles that have become names. It starts Cre _____ or. KF

  110. 110
    kairosfocus says:

    F/N: As fine tuning has come up, a point of reference:

    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.]

    more on the anthropic principle from Lewis and Barnes https://uncommondescent.com/intelligent-design/hitchhikers-guide-authors-puddle-argument-against-fine-tuning-and-a-response/#comment-729507

    KF

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