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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

Comments
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.]
kairosfocus
October 14, 2022
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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. KFkairosfocus
October 14, 2022
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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.Sir Giles
October 14, 2022
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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/kairosfocus
October 14, 2022
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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.Alan Fox
October 14, 2022
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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. KFkairosfocus
October 14, 2022
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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?Alan Fox
October 14, 2022
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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 . . .kairosfocus
October 14, 2022
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Kairosfocus: we both know that we are dealing with an algorithm. What triggers the algorithm? Does it run all the time?JVL
October 14, 2022
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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.Alan Fox
October 14, 2022
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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. KFkairosfocus
October 14, 2022
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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.Alan Fox
October 14, 2022
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AF, we both know that we are dealing with an algorithm. KFkairosfocus
October 14, 2022
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How is not why, KF. BTW, as you claim to know better than I do, what precisely is my view?Alan Fox
October 14, 2022
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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. KFkairosfocus
October 14, 2022
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So now you claim is that DNA is written in machine code??? Goodness me!Alan Fox
October 14, 2022
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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. KFkairosfocus
October 14, 2022
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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.Alan Fox
October 14, 2022
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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.Alan Fox
October 14, 2022
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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 tooAlan Fox
October 14, 2022
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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. KFkairosfocus
October 14, 2022
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Also , if I give you a DNA sequence, can you tell me what it says?Alan Fox
October 14, 2022
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Tell me a word in DNA language. Put it in a sentence.Alan Fox
October 14, 2022
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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. KFkairosfocus
October 14, 2022
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...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.Alan Fox
October 14, 2022
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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. KFkairosfocus
October 14, 2022
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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 levelsAlan Fox
October 14, 2022
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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.Alan Fox
October 14, 2022
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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?Alan Fox
October 14, 2022
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Calling Seversky . . .kairosfocus
October 14, 2022
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