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L&FP, 63: Do design thinkers, theists and the like “always” make bad arguments because they are “all” ignorant, stupid, insane or wicked?

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Dawkins’ barbed blanket dismissiveness comes up far too often in discussions of the design inference and related themes. Rarely, explicitly, most often by implication of a far too commonly seen no concessions, selectively hyperskeptical policy that objectors to design too often manifest. It is time to set this straight.

First, we need to highlight fallacious, crooked yardstick thinking (as exposed by naturally straight and upright plumb-lines). And yes, that classical era work, the Bible, is telling:

Notice, a pivotal point here, is self-evident truths. Things, similar to 2 + 3 = 5:

Notoriously, Winston Smith in 1984 is put on the rack to break his mind to conform to The Party’s double-think. He is expected to think 2 + 2 = whatever The Party needs at the moment, suppressing the last twisted answer, believing that was always the case, while simultaneously he must know that manifestly 2 + 2 = 4 on pain of instant absurdity. This is of course a toy example but it exposes the way crooked yardstick thinking leads to chaos:

Of Lemmings, marches of folly and cliffs of self-falsifying absurdity . . .

(Yes, real lemmings do not act like that. But, humans . . . that’s a whole other story.)

So, now, let us turn to a recent barbed remark by one of our frequent objectors and my reply, laying out a frame of thought and inviting correction — dodged, of course:

KF, 120 in the Foundations thread: [[It is now clear that SG is unwilling to substantially back up the one liner insinuation he made at 84 above, try making a good argument. Accordingly, let me respond in outline, for record, to the general case, that people like us are ignorant, stupid, insane or wicked and the associated zero concessions, selectively hyperskeptical dismissiveness policy. Here, I will show the rational responsibility of the design inference and related ideas, views and approaches, for record and reference:

I will use steps of thought:

1: Reason, in general: Notice, supporters and fellow travellers of evolutionary materialistic scientism undermine the responsible, rational freedom required for reason to be credible. They tend to discount and discredit objectors, but in fact their arguments and assertions are self-referentially incoherent, especially reduction of mind to computationalism on a wetware substrate. Reppert is right to point out, following Haldane and others:

. . . let us suppose that brain state A [–> notice, state of a wetware, electrochemically operated computational substrate], which is token identical to the thought that all men are mortal, and brain state B, which is token identical to the thought that Socrates is a man, together cause the belief [–> concious, perceptual state or disposition] that Socrates is mortal. It isn’t enough for rational inference that these events be those beliefs, it is also necessary that the causal transaction be in virtue of the content of those thoughts . . . [But] if naturalism is true, then the propositional content is irrelevant to the causal transaction that produces the conclusion, and [so] we do not have a case of rational inference. In rational inference, as Lewis puts it, one thought causes another thought not by being, but by being seen to be, the ground for it. But causal transactions in the brain occur in virtue of the brain’s being in a particular type of state that is relevant to physical causal transactions.

2: This extends to Marx’s class/cultural conditioning, to Freud’s potty training etc, to Skinner’s operant conditioning , to claims my genes made me do it, and many more. So, irrationality and undermining of the credibility of reason are a general issue for such supporters and fellow travellers, it is unsurprising to see projection to the despised other (a notorious defence mechanism) and linked failure to engage self referentiality.

3: First principles of right reason: Classically, the core of reason starts with distinct identity, excluded middle, non contradiction. Something x is what it is i/l/o its core characteristics, nothing can be both x and not x in the same sense and circumstances, any y in W = {x| ~x} will be x, ~x, not both or neither. And more. Claimed quantum counter examples etc actually are rooted in reasoning that relies on such. And yes, there have been enough objections that this has come up and is in UD’s Weak Argument Correctives. We leave it to objectors like SG to tell us whether they acknowledge such first principles of right reason: _______ and explain why ________ .

4: Self evidence: There are arguments that, once we have enough experience and maturity to understand [a sometimes big if], will be seen as true, as necessarily true and as true on pain of immediate absurdities on attempted denial. That error exists is a good case in point, and if one is able to see that the attempt to deny objectivity of knowledge for a given reasonably distinct field of thought such as morals or history or reality [metaphysics], or the physical world, or external reality, or in general, etc, one is claiming to objectively know something about that field and so refutes oneself.

5: self referential incoherence and question begging: We just saw an example of how arguments and arguers can include themselves in the zone of reference of an argument in ways that undermine it, often by implying a contradiction. Such arguments defeat themselves. Question begging is different, it assumes, suggests or imposes what should be shown and for which there are responsible alternatives. Arguments can be question begging, and then may turn out to be self refuting.

6: Deduction, induction, abduction (inference to the best [current] explanation [IBE]) and weak-form knowledge: Deduction uses logical validity to chain from givens to conclusions, where if givens are so and the chain valid, conclusions must also be true. Absent errors of reasoning, the debate rapidly becomes one over why the givens. Induction, modern sense, is about degree of support for conclusions i/l/o evidence of various kinds as opposed to demonstration, statistics, history, science, etc are common contexts. Abduction, especially IBE, compares live option alternatives and what they imply, on factual adequacy, coherence and balance of explanatory power, to choose the best explanation so far. In this context weak sense common knowledge is warranted, credibly true (so, reliable) belief. Which, is open to correction or revision and extension.

7: Worldviews context: Why accept A? B. But why B? C, etc. We see that we face infinite regress, or circularity or finitely remote first plausibles . . . which, frame our faith points . . . as we set out to understand our world. Infinite regress is impossible to traverse in reasoning or in cause effect steps, so we set it aside, we are forced to have finitely remote start points to reasoning and believing, warranting and knowing — first plausibles that define our views of the world. Thus, we all live by faith, the question is which, why; so, whether it is rational/reasonable and responsible. Where, too, all serious worldview options bristle with difficulties, hence the point that philosophy is the discipline that studies hard, basic questions. Question begging circles are a challenge, answered through comparative difficulties across factual adequacy, coherence and balance of explanatory power: elegantly simple, neither ad hoc nor simplistic.

[Let’s add an illustration:]

A summary of why we end up with foundations for our worldviews, whether or not we would phrase the matter that way}

[or in Aristotle’s words:]

8: Failure of evolutionary materialistic scientism and fellow traveller views: It will be evident already, that, while institutionally and culturally dominant, evolutionary materialistic scientism and fellow travellers are profoundly and irretrievably incoherent. Yes, a view backed by institutions, power brokers in the academy, the education system and the media can be irretrievably, fatally cracked from its roots.

9: Logic of being (and of structure and quantity), also possible worlds: Ontology and her grand child, Mathematics, grow out of core philosophy, particularly distinct identity and consideration of possible worlds. A possible world, w, is a sufficiently complete description of how our world or another conceivable or even actual world is or may be; i.e. a cluster of core, world describing propositions. In that context, a candidate being or entity or even state of affairs, c, can be impossible of being [e.g. a Euclidean plane square circle] or possible. Possible beings may be contingent [actual in at least one possible world but not all] or necessary [present in every possible world]. We and fires are contingent, dependent for existence on many independent, prior factors; what begins or may cease of existence is contingent. Necessary beings are best seen as part of the fabric or framework for this or any possible world. We can show that distinct identity implies two-ness, thence 0, 1, 2. Ponder, W = {A|~A}, the partition is empty, 0, A is a unit, ~A is a complex unit, so we see 2. So, onward via von Neumann’s construction, the counting numbers N. Thence, Z, Q, R, C, R* etc in any w. This is what gives core Mathematics its universal power.

10: The basic credibility of the design inference: of course, we routinely recognise that many things show reliable signs of intelligently directed configuration as key cause, i.e. design. For example, objectors to the design inference often issue copious, complex text in English, beyond 500 to 1,000 bits of complexity. In the 70’s Orgel and Wicken identified a distinct and quantifiable phenomenon, functionally specific, complex organisation and/or associated information, which I often abbreviate FSCO/I. Organisation is there as things like a fishing reel [my favourite, e.g. the ABU 6500 CT] or a watch [Paley, do not overlook his self replicating watch thought exercise in Ch 2]

or an oil refinery or a computer program [including machine code]

Petroleum refinery block diagram illustrating FSCO/I in a process-flow system

or the cell’s metabolic process-flow network [including protein synthesis]

[with:]

Step by step protein synthesis in action, in the ribosome, based on the sequence of codes in the mRNA control tape (Courtesy, Wikipedia and LadyofHats)

[and:]

all can be described in a suitably compact string of Y/N questions, structured through description languages such as AutoCAD. The inference posits that, with trillions of cases under our belt, reliably, FSCO/I or its generalisation, CSI, will be signs of design as key cause. The controversies, as may be readily seen, are not for want of evidence or inability to define or quantify, but because this challenges the dominant evolutionary materialism and fellow travellers. Which, of course, long since failed through irretrievable self referential incoherence.
_____________________

So, challenge: let SG and/or others show where the above fails to be rational and responsible, if they can__________________ Prediction, aside from mere disagreement and/or dismissiveness, assertions, or the trifecta fallacy of red herrings, led away to strawmen soaked in ad hominems and set alight to cloud, confuse, poison and polarise the atmosphere, they will not be able to sustain a case for general failure to be rational and responsible.]]

The good argument challenge is duly open for response. END

U/D, Nov 4: As it seems certain objectors want to attack the descriptive metaphor, islands of function amidst seas of non function, let me put up here a couple of infographics I used some years ago to discuss this concept. But first, as the primary contexts have to do with protein synthesis and OoL, let me first put up Vuk Nicolic’s video illustrating just what is required for protein synthesis:

. . . and Dr James Tour’s summary presentation on OoL synthesis challenges:

Now, this is my framework for discussing islands of function:

. . . and, on associated active information:

Thus, we can discuss the Orgel-Wicken functionally specific, complex organisation and associated information concept, FSCO/I, similarly:

We see here the needle in a haystack, blind search challenge and how it is dominated by not the hill climbing on fitness functions that is commonly discussed but by the issue of arriving at shorelines of first function. Obviously and primarily, for origin of cell based life [cf. Tour] but also to move from that first unicellular body plan to others. Where, we can observe too that even within an island of function, incremental changes will be challenged by intervening valleys, tending to trap on a given peak or plateau.

But, what of the thesis, that there is in effect a readily accessible first functionality, incrementally connected to all major body plans, allowing unlimited, branching tree of life body plan level macro evolution?

The Smithsonian’s tree of life model, note the root in OOL

Obviously, this architecture implies such continuity. The first problem, obviously is the root and the plethora of speculations and debatable or even dubious syntheses that have been made into icons of the grand evolutionary narrative and taught as effective fact, already tell us something is wrong. A second clue is how the diagram itself implies that transitional forms should utterly dominate the space, with terminal tips being far less common. On basic statistics, we should then expect an abundance of these transitions or “links.” The phrase, missing link, tells the tale instead.

For, the trade secret of paleontology, is the utter rarity of such forms, to the point where punctuated equilibria was a major school intended to explain that general absence. Where, Darwin, notoriously, noted the gaps but expected and predicted that on wider investigations they would go away. But now, after 150 years of searching, billions of fossils seen in situ, millions in museum back office drawers [only a relative few can be displayed] and over a quarter of a million fossil species, the pattern of gaps is very much still here, hot denials and dismissals notwithstanding. That is especially true of the Cambrian fossil life form revolution, where the major current body plans for animals pop up with nary an intermediate. So much so, that there have been significant efforts to make it disappear, obfuscating its significance.

We also have molecular islands of function, starting with protein fold domains. Thousands, scattered across the AA sequence space, no easy path connecting them. Even just homochirality soon accumulates into a serious search space challenge as molecules are complex and mirror image handedness is not energetically enforced, why racemic forms, 50-50 mixes of left and right handed molecules are what we tend to get in lab syntheses. This then gets more complicated where there are multiple isomers as Tour discusses.

In short, a real issue not a readily dismissible notion without significant empirical support.

And so forth.

U/D2 Nov 4: I just found where I had an image from p. 11 NFL, so observe:

ID researcher William A Dembski, NFL, p.11 on possibilities, target zones and events

Where, we can further illustrate the beach of function issue:

And, some remarks:

U/D 3 Nov 7: The all-revealing Eugenics Conference Logo from 1912 and 1921 showing how it was seen as a capstone of ever so many sciences and respected domains of knowledge, especially statistics, genetics, biology and medicine, even drawing on religion, with, politics, law, education, psychology, mental testing and sociology . . . menacingly . . . also being in the roots:

“Eugenics is the self-direction of human evolution”: Logo from the Second International Eugenics Conference, 1921, depicting Eugenics as a tree which unites a variety of different fields.

U/D 4, Nov 10: A reminder on cosmological fine tuning, from Luke Barnes:

Barnes: “What if we tweaked just two of the fundamental constants? This figure shows what the universe would look like if the strength of the strong nuclear force (which holds atoms together) and the value of the fine-structure constant (which represents the strength of the electromagnetic force between elementary particles) were higher or lower than they are in this universe. The small, white sliver represents where life can use all the complexity of chemistry and the energy of stars. Within that region, the small “x” marks the spot where those constants are set in our own universe.” (HT: New Atlantis)

U/D 5, Nov 12: As there is dismissiveness of the textual, coded information stored in DNA, it is necessary to show here a page clip from Lehninger, as a case in point of what should not even be a debated point:

For record.

U/D 6, Nov 14: The per aspect design inference explanatory filter shows how right in the core design inference, alternative candidate causes and their observational characteristics are highlighted:

Again, for record.

Comments
Relatd, 448, good reference to an oldie but goodie. Molecular scale nanotechnology is an emerging world of technology, even IC features are approaching that scale now. KFkairosfocus
November 12, 2022
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Jerry, all science is science+, it is embedded in the name. "Science" is the Latin word for knowledge, and knowledge is inherently a philosophical issue, strongly pivoting on logic, epistemology and logic of being [ontology] issues. The issues surface when there is need to discuss disagreements, but in what Kuhn called normal science, it is under the surface. That points to the closely tied discipline, philosophy of science, often with further context in history of science which provides key grist for the mill. Then too, once science affects worldviews, ideologies and cultural/policy agendas, politically oriented issues arise. A classic example was eugenics and associated issues, which seemed to be a steamroller of progress (as is noted in the u/d 4 to OP) but turned out instead to be a gateway to horrific disaster by way of voyages of folly on the ship of state. KF PS, these issues of course tie into fundamental, first principles and duties of reasoning, and to our nature as rational, responsible, significantly free creatures. The tendency to reduce rational mind to computation on a GIGO-controlled substrate, programmed God knows how, is self referential and self undermining as J B S Haldane pointed out long ago. How we can be and know we are rational, responsible and significantly free points onward to the roots and nature of reality. The principle of distinct identity that A is A i/l/o core [and coherent] characteristics ties to the nature of being thus possible/impossible and contingent/necessary being, etc, carrying with it the close corollaries non contradiction and excluded middle. Our rational first duties point to how in the end we cannot sever moral government from the root of reality, it is only in the roots that the is-ought gap can be successfully bridged. And much more.kairosfocus
November 12, 2022
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JVL, machine code is machine-executable code, one step above the physical level in the usual layer cake stack of virtual machines riding on the hardware. It is often in read only form, once adequately defined. Well do I remember the days of developing a two port memory board to serve as a ROM emulator [with cassette tape as magnetic tape backing store, much cheaper than the old refrigerator sized tape drives!] then burning to EPROM once more or less finalised. As in, ROM burners and UV erasers, with metal foil tape or stickers to protect from erasure. Q is of course right to point to other levels of information storage, but we here focus a key case, protein assembly codes and the assembly machines they control. More, later. KF PS, wiki confesses, regarding firmware:
In computing, firmware is a specific class of computer software that provides the low-level control for a device's specific hardware. Firmware, such as the BIOS of a personal computer, may contain basic functions of a device, and may provide hardware abstraction services to higher-level software such as operating systems. For less complex devices, firmware may act as the device's complete operating system [--> in the old days, the monitor], performing all control, monitoring and data manipulation functions. Typical examples of devices containing firmware are embedded systems (running embedded software), home and personal-use appliances, computers, and computer peripherals. Firmware is held in non-volatile memory devices such as ROM, EPROM, EEPROM, and Flash memory. Updating firmware requires ROM integrated circuits to be physically replaced, or EPROM or flash memory to be reprogrammed through a special procedure.[1] Some firmware memory devices are permanently installed and cannot be changed after manufacture. Common reasons for updating firmware include fixing bugs or adding features to the device.
kairosfocus
November 12, 2022
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ID is Science+ So if you believe science fiction is real, then you are anti ID.jerry
November 12, 2022
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SG at 447, There is no weakness. https://intelligentdesign.org/articles/molecular-machines-in-the-cell/relatd
November 12, 2022
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Relatd: An accurate description of Intelligent Design.
I know. And that is its weakness.Sir Giles
November 12, 2022
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Kairosfocus @443, Nicely elaborated, however, I don't know why you bother replying to JVL. JVL provides no support for the majority of his assertions and negations, makes stuff up, denies his ignorance when pointed out to him, and then picks nits on definitions. For example, when he asserts that DNA has no RAM storage, he's apparently referring LITERALLY to Random Access Memory CHIPS specifically rather than by analogy. He's blissfully unaware of heritable epigenetic programming from environmental stresses. The fact that information can be carried and stored by a succession of different technologies and media appears completely beyond his comprehension! For example, theoretical physicist Dr. James Gates talks about "computer codes" he discovered in buried in the equations used to describe the cosmos here: https://www.youtube.com/watch?v=oc4GOkHfxBY Dr. Gates wasn't referring to microprocessor CHIPS floating in the cosmos, but the processing of specific types of digital instructions and error correction. Let me note that Dr. Gates later corrected his reference to Shannon Information, which should have been "Hamming codes." JVL's lost the argument multiple times, but keeps getting up and claiming victory, spamming UD with endless number of posts and ad hominem attacks. So, my suggestion is to please continue posting your observations, but simply ignore the trollbots. -QQuerius
November 12, 2022
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Kairosfocus: I comment in steps of thought and — SG’s crackling under the pot notwithstanding — will enumerate for reference. I don't mind, whatever trips your trigger. As are protein assembly codes in DNA sections that act as such a store, here a string data structure tape. Read only! Not dynamic, writeable memory as exists with machine coding. DNA AA coding segments are read in a particular order of three base codons, based on the relevant dialect of the genetic code. Each gene is but what forces the sequences that genes are read in unlike in machine code when every single line of code that is read is in a proscribed order. Each line carries out a function that might be completely different from the line above and I don't just mean different like a different protein. I mean different as in retrieving a value, changing a value, storing a value, comparing values, swapping values, etc. DNA 'instructions' are all of the same type: create these molecules in this order then stop. Nothing at all like machine code. There are classically three main program structures and a fourth that is derivative: sequence, branch, loop, case. The only one that is vaguely like DNA is sequence. Vaguely.l There is no requirement that any particular program must branch or loop or it is not a program, it fails to execute an algorithm. The program branches or loops depending on the input and the values calculated. DNA does none of those. It doesn't loop or branch or take input values and do calculations upon them. A gene is 'off' or 'on', it' is transcribed or it isn't. Period. Nor is testing that a loop exit condition is met a requisite for halting. Halting is a requirement in its own right. Each gene has a stop code but there is no overall program in DNA that needs to be started and stopped. DNA is not like machine code. You set up a branching and looping red herring and strawman, fail. Each gene is either 'on' or 'off'; it's transcribed or it isn't. And, guess what, many are transcribed AT THE SAME TIME, again, unlike machine code. Not a requirement, again. If a simple elegant sequence will do the job and resides in read only memory, that is more than good enough. Not the point. The point is DNA is NOT like machine code, not that it's good enough. Computer programs are created to take in input and then do something, the something might be different depending on the input. DNA is not like that. Can is the key term, that needs not be the case, and as we both know DNA protein codes are INPUTS in their own right for NC machines, ribosomes. Genes are 'on' or 'off', if they're 'on' their sequence is transcribed and the end result is that proteins are created. The 'inputs' do not vary, they do not come from an 'operator'. In fact, the whole point of writing computer programs is to deal with different inputs. If we only had to solve a problem once or twice there would be no point in writing code that can do different things depending on what input is given. Again, not a requisite, many embedded systems do not have displays, many NC machines do not have displays. There is no point in writing computer code if the result of the code is not used or displayed or sent somewhere. DNA’s stored information in the form of protein codes, are causal, contributory factors to the working of ribosomes. Does that make it like machine codes? An outright blunder. DNA in this aspect stores protein codes, and has been repurposed to store general digital information as has been noted here at UD. DNA is a read-only storage medium but 'executing' DNA sequences does not take in values, change values or store values. Something that machine coding IS DESIGNED TO DO. Again, no one would write a computer program just to follow a bunch of steps. A player piano can do that. That's not machine code, that's just a to do list. This last makes it obvious that part of the intransigence is refusal on the part of objectors to attend to inconvenient facts. I have pointed out many, many, many ways that DNA and DNA processing is NOT like computer programming or computer language processing. I fully expect you to keep hammering away at the few, minor points of overlap but think about this: can you write a computer program in DNA that executes in a cell? One that I can give a different input to and I will get a different result? One that I can input a value to and get a value back that I can read or interpret or use? One that I can fire up, at will, and pull the plug if it goes haywire? Not a requisite of serving as memory or holding code. But one of the major points of bothering to write machine code. Quite often ROM is fixed, it holds core code that is there to be executed not altered. Exactly, like DNA you cannot create variables, put values into those variables, change those values and, finally, export those values. DNA IS NOT MACHINE CODE. In almost all ways it's nothing like machine code. Any computer programmer can see that. Maybe very early computer programs were just lists of instructions executed in order, the closest thing to that is individual genes in DNA but that's so elementary, that is at the level of a player piano. AND genes cannot work with variables. Even the very early computer programs could take a value, have each line of code pick up the value from the line before, change it and then store it for the next line to pick up. DNA does not store anything!! It has no RAM to work with. That is so fundamental . . . I'm sure you will gloss over that but that is why your analogy breaks down at the very basic level.JVL
November 12, 2022
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F/N: For record, I have placed as U/D 5, the image from a page in Lehninger, to help illustrate just how off base the objections we are seeing are.kairosfocus
November 12, 2022
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JVL, I comment in steps of thought and -- SG's crackling under the pot notwithstanding -- will enumerate for reference. >>machine code is stored in particular locations in memory>> 1: As are protein assembly codes in DNA sections that act as such a store, here a string data structure tape. >> in such a way that when a particular program is launched the lines of code are read in a particular order.>> 2: DNA AA coding segments are read in a particular order of three base codons, based on the relevant dialect of the genetic code. >>Within the code the order may be changed, and frequently sections are repeated until a certain condition is met.>> 3: There are classically three main program structures and a fourth that is derivative: sequence, branch, loop, case. 4: There is no requirement that any particular program must branch or loop or it is not a program, it fails to execute an algorithm. 5: Nor is testing that a loop exit condition is met a requisite for halting. Halting is a requirement in its own right. >> That’s not how DNA works. >> 6: You set up a branching and looping red herring and strawman, fail. >>Also, machine code stores, alters and retrieves values in memory,>> 7: Not a requirement, again. If a simple elegant sequence will do the job and resides in read only memory, that is more than good enough. >> it can even take input from outside the computer. >> 8: Can is the key term, that needs not be the case, and as we both know DNA protein codes are INPUTS in their own right for NC machines, ribosomes. >>Some of those values control when other lines of code are executed if at all. >> 9: More on the branching red herring. >>Some of those values are ‘displayed’ >> 10: Again, not a requisite, many embedded systems do not have displays, many NC machines do not have displays. >>or cause some peripheral device to carry out a series of actions.>> 11: DNA's stored information in the form of protein codes, are causal, contributory factors to the working of ribosomes. >> DNA does not ‘store’ anything.>> 12: An outright blunder. DNA in this aspect stores protein codes, and has been repurposed to store general digital information as has been noted here at UD. 13: This last makes it obvious that part of the intransigence is refusal on the part of objectors to attend to inconvenient facts. >>DNA does not ‘display’ anything.>> 14: Not a requisite of serving as memory or holding code. >>DNA does not and cannot alter anything in ‘storage’.>> 15: Quite often ROM is fixed, it holds core code that is there to be executed not altered. KFkairosfocus
November 12, 2022
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Kairosfocus: we are looking at machine code instructions, that is not even a serious issue, No, we are NOT looking at machine code instructions. They are not stored like machine code, they are not executed like machine code, they do not have the capacity to set and change memory locations like machine code, they don't take external inputs like machine code. I don't care if Dr Lehninger said it or not, instead of just blindly accepting anything that supports your preheld view that humans are part of a selective breeding program just think about the situation yourself. This link has an actual image from a key page comparing text on a stele with DNA. An actual image!! Oh my. Be still my beating heart. OH, by the way, you have never attempted to consider whether or not humans might be just another transitional species on the way to some ultimate goal. Does that idea stick in your craw? You couldn't possibly be a rung or two down on the ladder could you? you know full well that humans, as contingent creatures, exemplify but do not exhaust the possibilities for intelligence or intelligently directed configuration. So they could not be the ultimate goal. Thank you. The crude abuses of induction that try to pretend otherwise need to account for why something like SETI exists What? And indeed, we have actually already repurposed DNA to store other general purpose digital information as has been notified here. Not the same as machine code though. For, there is a whole political movement expressing fears over genetic modification of organisms. So? What does that have to do with anything?JVL
November 12, 2022
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SG, you know full well that humans, as contingent creatures, exemplify but do not exhaust the possibilities for intelligence or intelligently directed configuration. The crude abuses of induction that try to pretend otherwise need to account for why something like SETI exists. And indeed, we have actually already repurposed DNA to store other general purpose digital information as has been notified here. More to the point, Venter et al show that relevant molecular nanotech technologies exist, work and are used in genetic engineering, another point where this flimsy argument falls apart. For, there is a whole political movement expressing fears over genetic modification of organisms. KFkairosfocus
November 12, 2022
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PM1, we are looking at machine code instructions, that is not even a serious issue, see the clip below from Lehninger as just one witness if you need biochem guys to say it. But we don't actually need to go there. The ribosome assembles AA chains, stepwise, to create proteins. The instructions are stored in DNA sections, are transcribed and sometimes edited to make mRNA. Then AUG, start and load methionine. Elongate with AA no 2, 3 . . . in successive sequence, stop. Coded algorithm, start, stepwise process towards a goal, halting. Yes, it uses molecular nanotech based on pretty sophisticated polymer chemistry, but COMPUTATIONAL PROCESSES DO NOT CHANGE BASED ON THE TECHNOLOGY THAT EFFECTS THEM. Instantiation, not crude and suspect analogy. KF PS, Lehninger -- and for 50 years or so that has been a serious name indeed:
"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/ (This link has an actual image from a key page comparing text on a stele with DNA.)kairosfocus
November 12, 2022
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SG at 437, An accurate description of Intelligent Design.relatd
November 12, 2022
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SG at 429, "... part of my job involves training companies on how to document procedural documents as part of their management system." Sounds like Intelligent Design.relatd
November 12, 2022
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ID proponents falsely take advantage of our often anthropocentric use of language when describing biology. 1) The DNA code. The only confirmed source of codes is human intelligence therefore the DNA code is the result of intelligence. 2) The flagellum operates like a rotary engine. The only confirmed source of rotary engines is human intelligence therefore the flagellum is designed.Sir Giles
November 12, 2022
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PyrrhoManiac1: And that matters to this debate since KF has been insisting that the main reason why we reject the use of engineering concepts in molecular biology is because of our “selective hyperskepticism” (as he calls it) and refusal to abide by basic epistemic norms. He's not so good with dissension. Another problem with the DNA vs machine code analogy is . . . DNA is 'interpreted' via various chemical affinities with no need to go through different bits of wiring. Machine code is 'interpreted' by having part of the operating system read the particular instruction, accessing the particular part of the hardware that interprets that instruction which then does whatever it's supposed to do. Once that instruction is done and dusted, the system moves onto the next instruction which may access a different bit of hard wired on-off gates. Again, the analogy doesn't hold. DNA is NOT close enough to machine code to reach an automatic conclusion that it's designed.JVL
November 12, 2022
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@434
Especially since Cicero didn’t know much about biology or computer science.
True, but my point is that one can (and I would say should) endorse the basic rules of reasoned argument -- which KF has been calling "Ciceronian principles of right reason" -- while also thinking that engineering concepts really don't work in molecular biology. And that matters to this debate since KF has been insisting that the main reason why we reject the use of engineering concepts in molecular biology is because of our "selective hyperskepticism" (as he calls it) and refusal to abide by basic epistemic norms.PyrrhoManiac1
November 12, 2022
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PyrrhoManiac1: weird to think you'd have to number pyro maniacs . . .. one can reject the use of engineering concepts in biology without violating any Ciceronian principles of right reason. Especially since Cicero didn't know much about biology or computer science.JVL
November 12, 2022
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@431
For example: machine code is stored in particular locations in memory in such a way that when a particular program is launched the lines of code are read in a particular order. Within the code the order may be changed, and frequently sections are repeated until a certain condition is met. That’s not how DNA works. Also, machine code stores, alters and retrieves values in memory, it can even take input from outside the computer. Some of those values control when other lines of code are executed if at all. Some of those values are ‘displayed’ or cause some peripheral device to carry out a series of actions. DNA does not ‘store’ anything. DNA does not ‘display’ anything. DNA does not and cannot alter anything in ‘storage’.
Thank you for that brief explication of why DNA is not a computer program. I think it speaks to my point above that one can reject the use of engineering concepts in biology without violating any Ciceronian principles of right reason.PyrrhoManiac1
November 12, 2022
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@ JVL Precisely.Alan Fox
November 12, 2022
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Kairosfocus: I will note for record that trying to rhetorically mislabel observed long recognised code and algorithms for protein synthesis in the DNA and mRNA of the cell as an “analogy” simply underscores the bankruptcy of your objection. It is an analogy. Clearly, by definition, since it's not the same as the thing itself. Multiplied, by your fear of the significance of that well founded recognition, i.e. language as text expressing protein assembly instructions is embedded in the cell, and further expresses a goal-directed process; both of which are strong signs of design. Too funny. You think I'm worried about taking one step in a direction and then falling down a slippery slope which lead to design. That is not true. I am pointing out that your analogies do not hold and, therefore, there is no slippery slope to design. As others have mentioned: you are only capable of seeing things from your point of view. I am pretty sure that if you saw such machine code for numerical control of a machine — here, that marvel of molecular nanotech, the ribosome and the use of mobile position arm devices with a universal tool tip, tRNA — you would readily recognise the case. I have seen computer machine code, AS I ALREADY TOLD YOU! And I know that the way that code is interpreted or used is not the same as the way DNA is 'read' in a cell. For example: machine code is stored in particular locations in memory in such a way that when a particular program is launched the lines of code are read in a particular order. Within the code the order may be changed, and frequently sections are repeated until a certain condition is met. That's not how DNA works. Also, machine code stores, alters and retrieves values in memory, it can even take input from outside the computer. Some of those values control when other lines of code are executed if at all. Some of those values are 'displayed' or cause some peripheral device to carry out a series of actions. DNA does not 'store' anything. DNA does not 'display' anything. DNA does not and cannot alter anything in 'storage'. It's an analogy. And the analogy breaks down quickly. It's obvious. Your problem is manifestly ideological, not evidence and not disputes over analogies as a form of modern sense inductive reasoning, argument by support not demonstration. Uh huh. OR, maybe, I'm a better biologist and a better computer scientist than you are. do you imagine that you can ignore what was done in answer to your challenges and pretend that I have not answered carefully on OoL, without consequences for your own credibility? You have tried to avoid saying that you think cells were the first form of life on earth. If that's wrong then, by all means, correct it. Actually, it doesn't matter . . . there are still no islands of functions. Because IF life on earth started as a single cell and everything else descended from that then all life forms on earth would be part of the same area of function. No islands. You haven't really thought this through have you? You think the designer has almost continually tweaked genomes over billions of years to create life forms that could not possibly have descended from what came before. If that were the case then why do we share so much chemistry? Why do we share so many diseases? Why can so many life forms consume other life forms and be nourished? You think in analogies all the time. But they break down under scrutiny. All models are wrong but some are more useful than others. Yours are not useful because not only do they not help us understand the data we have, they run contrary to the data we have.JVL
November 12, 2022
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Querius: [asked for] The number of identical changes required for fixing a variation in a population. and linked to a Wikipedia article discussing the basics. https://en.wikipedia.org/wiki/Fixation_(population_genetics) In that article the section called Probability discusses the pertinent mathematics. There is no required number of times an identical change has to be present for the allele to (eventually) get 'fixed'. As I already said: it could be the case that a single individual has the change and that can eventually get 'fixed'. It's possible that the mutation that allows for blue eyes happened once in one individual. Possible. Querius: [also asked] The maximum rate of random mutations. Obviously there could be no rate of mutations greater than 100% but clearly the mutation rate for most species and genome locations is far below that. Again, there is a Wikipedia article which discusses the basics: https://en.wikipedia.org/wiki/Mutation_rate Some excerpts:
The human mutation rate is higher in the male germ line (sperm) than the female (egg cells), but estimates of the exact rate have varied by an order of magnitude or more. This means that a human genome accumulates around 64 new mutations per generation because each full generation involves a number of cell divisions to generate gametes. Human mitochondrial DNA has been estimated to have mutation rates of ~3× or ~2.7×10?5 per base per 20 year generation (depending on the method of estimation); these rates are considered to be significantly higher than rates of human genomic mutation at ~2.5×10?8 per base per generation. Using data available from whole genome sequencing, the human genome mutation rate is similarly estimated to be ~1.1×10?8 per site per generation.
The rate for other forms of mutation also differs greatly from point mutations. An individual microsatellite locus often has a mutation rate on the order of 10?4, though this can differ greatly with length.
Some sequences of DNA may be more susceptible to mutation. For example, stretches of DNA in human sperm which lack methylation are more prone to mutation.
In general, the mutation rate in unicellular eukaryotes (and bacteria) is roughly 0.003 mutations per genome per cell generation. However, some species, especially the ciliate of the genus Paramecium have an unusually low mutation rate. For instance, Paramecium tetraurelia has a base-substitution mutation rate of ~2 × 10?11 per site per cell division. This is the lowest mutation rate observed in nature so far, being about 75× lower than in other eukaryotes with a similar genome size, and even 10× lower than in most prokaryotes. The low mutation rate in Paramecium has been explained by its transcriptionally silent germ-line nucleus, consistent with the hypothesis that replication fidelity is higher at lower gene expression levels.
The highest per base pair per generation mutation rates are found in viruses, which can have either RNA or DNA genomes. DNA viruses have mutation rates between 10?6 to 10?8 mutations per base per generation, and RNA viruses have mutation rates between 10?3 to 10?5 per base per generation.
Some of the formatting got lost, if you're confused look at the original article. Querius: [again asks] The estimated reproductive advantage of organisms with a particular mutation over those without it. I again refer to a Wikipedia article which is an introduction, in this case look at the section headed: By effect on fitness (harmful, beneficial, neutral mutations). https://en.wikipedia.org/wiki/Mutation#By_effect_on_fitness_(harmful,_beneficial,_neutral_mutations) From the article:
Large-scale quantitative mutagenesis screens, in which thousands of millions of mutations are tested, invariably find that a larger fraction of mutations has harmful effects but always returns a number of beneficial mutations as well. For instance, in a screen of all gene deletions in E. coli, 80% of mutations were negative, but 20% were positive, even though many had a very small effect on growth (depending on condition). Note that gene deletions involve removal of whole genes, so that point mutations almost always have a much smaller effect. In a similar screen in Streptococcus pneumoniae, but this time with transposon insertions, 76% of insertion mutants were classified as neutral, 16% had a significantly reduced fitness, but 6% were advantageous. This classification is obviously relative and somewhat artificial: a harmful mutation can quickly turn into a beneficial mutations when conditions change. Also, there is a gradient from harmful/beneficial to neutral, as many mutations may have small and mostly neglectable effects but under certain conditions will become relevant. Also, many traits are determined by hundreds of genes (or loci), so that each locus has only a minor effect. For instance, human height is determined by hundreds of genetic variants ("mutations") but each of them has a very minor effect on height, apart from the impact of nutrition. Height (or size) itself may be more or less beneficial as the huge range of sizes in animal or plant groups shows.
Attempts have been made to infer the distribution of fitness effects (DFE) using mutagenesis experiments and theoretical models applied to molecular sequence data. DFE, as used to determine the relative abundance of different types of mutations (i.e., strongly deleterious, nearly neutral or advantageous), is relevant to many evolutionary questions, such as the maintenance of genetic variation, the rate of genomic decay, the maintenance of outcrossing sexual reproduction as opposed to inbreeding and the evolution of sex and genetic recombination. DFE can also be tracked by tracking the skewness of the distribution of mutations with putatively severe effects as compared to the distribution of mutations with putatively mild or absent effect. In summary, the DFE plays an important role in predicting evolutionary dynamics. A variety of approaches have been used to study the DFE, including theoretical, experimental and analytical methods.
And there's more if anyone wants to read it. Since these articles were dead easy to find and also easy to read one wonders why Querius asks such questions? Just to waste someone's time?JVL
November 12, 2022
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KF: SG, you have yet to respond on actual substance, using that points are enumerated — ever seen a numbered paragraphs paper? [I think Word can still do it] — as an excuse to dismiss.
My God. You are incapable of admitting error even on things that are easily verified. Enumeration in the way you do is not commonly used anywhere. And, yes, I am very familiar with numbered paragraph papers. I am in the last stages (FDIS) of revising an ISO standard (ISO/IEC 17043) as part of a CASCO working group. They are also common in the drafting of procedural documents. I know this because part of my job involves training companies on how to document procedural documents as part of their management system. Numbered paragraphs are used in a nested sequential manner. Each section is incremented (1, 2, 3…)and then each paragraph within each section is incrementally numbered, starting at #.1, #.2, etc. That is not what you are doing. For the love of Christ, why can’t you simply admit an error when you have been unequivocally corrected rather than doubling, tripling and quadrupling down?Sir Giles
November 12, 2022
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Go study up on the subject before posting more nonsense.
Oh, the irony! @JVL No, Querius isn't going to tell you where he got the straw for his strawman versions of evolutionary processes*. You might just as well ask him (or anyone else here) for any alternative ID explanation and expect an answer. *My best guess is he made them up.Alan Fox
November 12, 2022
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@426
language as text expressing protein assembly instructions is embedded in the cell, and further expresses a goal-directed process; both of which are strong signs of design. I am pretty sure that if you saw such machine code for numerical control of a machine — here, that marvel of molecular nanotech, the ribosome and the use of mobile position arm devices with a universal tool tip, tRNA
There is no shirking of basic epistemic duties in disagreeing about the relevance of engineering concepts for describing and explaining the processes of molecular biology.PyrrhoManiac1
November 12, 2022
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JVL, I will note for record that trying to rhetorically mislabel observed long recognised code and algorithms for protein synthesis in the DNA and mRNA of the cell as an "analogy" simply underscores the bankruptcy of your objection. Multiplied, by your fear of the significance of that well founded recognition, i.e. language as text expressing protein assembly instructions is embedded in the cell, and further expresses a goal-directed process; both of which are strong signs of design. I am pretty sure that if you saw such machine code for numerical control of a machine -- here, that marvel of molecular nanotech, the ribosome and the use of mobile position arm devices with a universal tool tip, tRNA -- you would readily recognise the case. Your problem is manifestly ideological, not evidence and not disputes over analogies as a form of modern sense inductive reasoning, argument by support not demonstration. KFkairosfocus
November 12, 2022
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SG, you have yet to respond on actual substance, using that points are enumerated -- ever seen a numbered paragraphs paper? [I think Word can still do it] -- as an excuse to dismiss. Negative credibility confirmed. The thorns are crackling away under the pot. KF VL, yes, there is a definite rhetorical pattern favoured by too many objectors, red herrings [pouncing on enumerated points!], led away to strawman caricatures [such enumeration is used to somehow discredit! while evading substance] soaked in ad homs [ridicule], clouding, choking, poisoning atmosphere for discussion. Seen far, far too often. And utterly revealing on intellectual bankruptcy. KFkairosfocus
November 11, 2022
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JVL @385,
Querius: Darwinian evolution begins with random mutations as I detailed here: JVL: Again, you emphasise random mutations without mentioning cumulative selection.
Yes, of course. Silly me, I thought it was obvious that without BEGINNING with random mutations, natural selection (cumulative selection supposedly forms from a series of single-step selections) is pointless. But you apparently think otherwise with your relentless unsupported assertions.
Querius: Notice that I’d written that the theory of evolution BEGINS WITH random mutation. It’s like JVL never bothered to read and respond to what I’d actually written instead of just making things up. JVL: Yes, I did read what you wrote and, yes, you continually focus on random mutations and leave out cumulative selection.
What is it about the words “begins with” that you can’t comprehend? See above.
Querius: The number of identical changes required for fixing a variation in a population. JVL: What do you mean? Sometimes it only take one change which is then handed down to offspring. You ask questions which make it sound like you don’t understand how things work.
Nope. For an introduction on the subject, see https://en.wikipedia.org/wiki/Fixation_(population_genetics)
Querius: The maximum rate of random mutations. JVL: Measured how? Against what?
Look it up yourself. I’m not your homework slave. J.B.L. Haldane pioneered this. Don’t you know anything about the theory of evolution?
Querius: The estimated reproductive advantage of organisms with a particular mutation over those without it. JVL: Really? Again, please be clearer. Do you mean the estimated average against all possible single point mutations?
Again, look it up yourself.
Querius: Notice that my alleged “poor interpretations” of the statements from the University of California website on evolution are conspicuously absent. JVL: Anyone can copy and paste but did you actually understand what you copied? I’m not so sure. The things you think we should know are poorly stated and confusing. I predict you will continue to argue about minutiae and gloss over your misunderstandings and misinterpretations thinking you’re being very profound and insightful.
Your parting ad hominem accusations indicate your admission of being owned. Go study up on the subject before posting more nonsense. -QQuerius
November 11, 2022
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Strawmen and red herrings soaked in oil of adhominems, and set ablaze? How does that phrase go? :-)Viola Lee
November 11, 2022
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