Uncommon Descent Serving The Intelligent Design Community

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
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.relatd
October 17, 2022
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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/releases/2009/06/090616103205.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/journal/v460/n7253/full/460415a.html
bornagain77
October 17, 2022
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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.jerry
October 17, 2022
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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.Alan Fox
October 17, 2022
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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.Alan Fox
October 17, 2022
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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?whistler
October 17, 2022
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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/doi/abs/10.1142/9789814508728_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/publications/the-unbearable-wholeness-of-beings
bornagain77
October 17, 2022
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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.Alan Fox
October 17, 2022
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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?whistler
October 17, 2022
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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.Alan Fox
October 17, 2022
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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 .whistler
October 16, 2022
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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?Alan Fox
October 16, 2022
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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.whistler
October 16, 2022
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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. Alan Fox
October 16, 2022
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AF, have you pondered singing, speaking, the vocal tract, thence words, language and encoded contextually sensitive meanings? Try, Sinach. KFkairosfocus
October 16, 2022
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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. :)whistler
October 15, 2022
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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/2011/11/with_a_startling_candor_oxford052821.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/2014/08/researchers_ran089231.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] https://uncommondescent.com/junk-dna/open-mike-cornell-obi-conference-chapter-11-not-junk-after-all-conclusion/ 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/content/pdf/1478-811X-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. … https://uncommondescent.com/genetics/gene-previously-linked-to-obesity-is-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).bornagain77
October 15, 2022
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@ Whistler The Krebs cycle, also called The Citric Acid Cycle, is central to cell respiration. https://en.m.wikipedia.org/wiki/Citric_acid_cycleAlan Fox
October 15, 2022
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@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.Alan Fox
October 15, 2022
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@Alan Fox : Could you explain a function (reproduction, respiration, digestion, etc.) only in terms of chemistry?whistler
October 15, 2022
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F/N: See Tour's response to a key critic here https://uncommondescent.com/intelligent-design/at-rice-u-dr-tour-exposes-the-false-science-behind-origin-of-life-research/kairosfocus
October 15, 2022
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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. KFkairosfocus
October 15, 2022
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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. KFkairosfocus
October 15, 2022
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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!Alan Fox
October 15, 2022
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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 :) )Sandy
October 15, 2022
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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. KFkairosfocus
October 14, 2022
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KF: SG, you know who is addressing and who is evading substance.
Yup. I am pretty sure it is clear to everyone.Sir Giles
October 14, 2022
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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].
kairosfocus
October 14, 2022
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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.]
kairosfocus
October 14, 2022
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KF: SG, predictable turnabout tactic…
Hmm. How was your rant different than
Label, assign motivation, polarize, dismiss, rinse, repeat.
Sir Giles
October 14, 2022
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