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L&FP, 62a: Science can rightly — and usefully — be viewed as “reverse engineering of the natural world”


Here, it is helpful to headline an update to L&FP, 62, as we need to return to a rich vein of thought that allows us to approach science in light of systems engineering perspectives:

[[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 Reverse Engineering-Forward Engineering 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.”]]

This approach is obviously design friendly and reflects commonplace views of many founders of modern science. For example, Johannes Kepler is commonly said to have written:

“I was merely thinking God’s thoughts after him. Since we astronomers are priests of the highest God in regard to the book of nature, it benefits us to be thoughtful, not of the glory of our minds, but rather, above all else, of the glory of God.”

Even were this apocryphal, it would be accurate to the views of many scientists then and now. However, the reverse engineering view is not merely of historical or philosophy of science interest. For, thanks to the works of such pioneers, we have a rich body of results that gives us confidence that such an approach builds on the framework of rational principles that have unfolded as we noted patterns in nature, inferred laws of nature and built explanatory models aka theories.

For telling instance, observe the ribosome in protein synthesis, showing a direct comparison to the role of punch paper tape and magnetic tape in the older generation of computers:

Such shows machine language in action. As Wikipedia confesses:

In computer programming, machine code is any low-level programming language, consisting of machine language instructions, which are used to control a computer’s central processing unit (CPU). Each instruction causes the CPU to perform a very specific task, such as a load, a store, a jump, or an arithmetic logic unit (ALU) operation on one or more units of data in the CPU’s registers or memory. Machine code is a strictly numerical language which is designed to run as fast as possible, and may be considered as the lowest-level representation of a compiled or assembled computer program or as a primitive and hardware-dependent programming language.

This is directly parallel — not merely, dismissibly loosely analogous to — the function of mRNA in the ribosome. Once threaded and aligned, we have AUG, START (and load Methionine), EXTEND (and load another specified AA), EXTEND . . . STOP. This is algorithmic procedure, and the code is based on a four state, prong height element similar to a Yale type, pin tumbler lock. But of course, using molecular nanotech with CG and AT or AU as complementary pairs:

This approach points onward to Wigner’s wondering about the uncanny effectiveness of mathematics in sciences. To this, my answer has been [see popular article here], that the logic of structure and quantity for possible worlds puts a core of Math into the structure of any feasible world. It only remains for us to explore and reverse engineer that structure then elaborate our own onward synthesis of bodies of knowledge.

Yes, Mathematics can also in key part be approached on reverse engineering, it’s not just Science here, indeed even logic as a technical discipline fits in. END

F/N: It is worth noting for reference record from Dan Peterson on the founding of modern science:
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.)]
KF kairosfocus
F/N: It is worth our while to highlight Newton's General Scholium to Principia:
. . . This most beautiful system of the sun, planets, and comets, could only proceed from the counsel and dominion of an intelligent and powerful Being. And if the fixed stars are the centres of other like systems, these, being formed by the like wise counsel, must be all subject to the dominion of One; especially since the light of the fixed stars is of the same nature with the light of the sun, and from every system light passes into all the other systems: and lest the systems of the fixed stars should, by their gravity, fall on each other mutually, he hath placed those systems at immense distances one from another. This Being governs all things, not as the soul of the world, but as Lord over all [--> sets aside pantheism and panentheism]; and on account of his dominion he is wont to be called Lord God pantokrator , or Universal Ruler; for God is a relative word, and has a respect to servants; and Deity is the dominion of God not over his own body, as those imagine who fancy God to be the soul of the world, but over servants. The Supreme God is [--> definition of God and his domain:] a Being eternal, infinite, absolutely perfect; but a being, however perfect, without dominion, cannot be said to be Lord God; for we say, my God, your God, the God of Israel, the God of Gods, and Lord of Lords; but we do not say, my Eternal, your Eternal, the Eternal of Israel, the Eternal of Gods; we do not say, my Infinite, or my Perfect: these are titles which have no respect to servants. The word God usually signifies Lord; but every lord is not a God. It is the dominion of a spiritual being which constitutes a God: a true, supreme, or imaginary dominion makes a true, supreme, or imaginary God. And from his true dominion it follows that the true God is a living, intelligent, and powerful Being; and, from his other perfections, that he is supreme, or most perfect. He is eternal and infinite, omnipotent and omniscient; that is, his duration reaches from eternity to eternity; his presence from infinity to infinity; he governs all things, and knows all things that are or can be done. He is not eternity or infinity, but eternal and infinite; he is not duration or space, but he endures and is present. He endures for ever, and is every where present; and by existing always and every where, he constitutes duration and space. Since every particle of space is always, and every indivisible moment of duration is every where, certainly the Maker and Lord of all things cannot be never and no where. Every soul that has perception is, though in different times and in different organs of sense and motion, still the same indivisible person. There are given successive parts in duration, co-existent puts in space, but neither the one nor the other in the person of a man, or his thinking principle; and much less can they be found in the thinking substance of God. Every man, so far as he is a thing that has perception, is one and the same man during his whole life, in all and each of his organs of sense. [--> identity issues] God is the same God, always and every where. He is omnipresent not virtually only, but also substantially; for virtue cannot subsist without substance. In him are all things contained and moved [i.e. cites Ac 17, where Paul evidently cites Cleanthes and sets him in a Biblical, Creation context]; yet neither affects the other: God suffers nothing from the motion of bodies; bodies find no resistance from the omnipresence of God. It is allowed by all that the Supreme God exists necessarily [--> necessary being]; and by the same necessity he exists always, and every where. [i.e accepts the cosmological argument to God, also implies God is framework to the world, one doubts possible world speak would have been well studied then.] Whence also he is all similar, all eye, all ear, all brain, all arm, all power to perceive, to understand, and to act; but in a manner not at all human, in a manner not at all corporeal, in a manner utterly unknown to us. As a blind man has no idea of colours, so have we no idea of the manner by which the all-wise God perceives and understands all things. He is utterly void of all body and bodily figure [--> issues of necessary being, not made up from detachable parts], and can therefore neither be seen, nor heard, or touched; nor ought he to be worshipped under the representation of any corporeal thing. [Cites Exod 20.] We have ideas of his attributes, but what the real substance of any thing is we know not. In bodies, we see only their figures and colours, we hear only the sounds, we touch only their outward surfaces, we smell only the smells, and taste the savours; but their inward substances are not to be known either by our senses, or by any reflex act of our minds: much less, then, have we any idea of the substance of God. We know him only by his most wise and excellent contrivances of things, and final cause [i.e from his designs]: we admire him for his perfections; but we reverence and adore him on account of his dominion: for we adore him as his servants; and a god without dominion, providence, and final causes, is nothing else but Fate and Nature. Blind metaphysical necessity, which is certainly the same always and every where, could produce no variety of things. [i.e necessity does not produce contingency] All that diversity of natural things which we find suited to different times and places could arise from nothing but the ideas and will of a Being necessarily existing. [That is, implicitly rejects chance, Plato's third alternative and explicitly infers to the Designer of the Cosmos.] But, by way of allegory, God is said to see, to speak, to laugh, to love, to hate, to desire, to give, to receive, to rejoice, to be angry, to fight, to frame, to work, to build; for all our notions of God are taken from. the ways of mankind by a certain similitude, which, though not perfect, has some likeness, however. And thus much concerning God; to discourse of whom from the appearances of things, does certainly belong to Natural Philosophy. [General Scholium to Principia, paragraphs added. Notice what he thought about discourse on God and Natural Philosophy.]
This shows the perspective of perhaps the most important founding figure in science. KF kairosfocus
Relatd, actually a major study of living organisms is by dissection and of course the reverse engineering of the PC was a key, software breakthrough. But more to the point, methodical per aspect exploration of features of our world are the basis for composing scientific theories and frameworks of knowledge. Quantum processes are also similarly explored. A mystique tends to apply, so, note that a fire is in key parts a quantum process. KF kairosfocus
"reverse engineering" usually refers to some type of mechanical artifact. Those with the appropriate skill take it apart to see how it works. This applies only somewhat to living things. A few scientists view them as mechanisms that are reducible to parts. That is not the case, especially when looking at human beings. All living things are connected to the quantum world. Subatomic processes are involved. So scientists who are attempting to create life in the lab can't do it. The best they've been able to manage is a 'minimal cell' that uses components they don't understand. Not fully. relatd
Yes, moving to possible worlds, core math and so core logic considered as an algebra or family of algebras, are also drawn into the reverse engineering view. kairosfocus
L&FP, 62a: Science can rightly — and usefully — be viewed as “reverse engineering of the natural world” kairosfocus

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